8XWZ | pdb_00008xwz

Non-crystalline proximal tubulopathy and crystalline cast nephropathy-causing Bence-Jones protein PT-CN: An entire immunoglobulin kappa light chain dimer

PDB DOI: https://doi.org/10.2210/pdb8XWZ/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2024-01-17 Released: 2025-01-22
Deposition Author(s): Ezawa, T., Otomo, R., Nozawa, K., Kyoya, S., Noguchi, K., Yohda, M., Odaka, M., Matsumura, H.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.257 (Depositor), 0.257 (DCC)
R-Value Work:
0.204 (Depositor), 0.205 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Multiple myeloma-associated non-crystalline proximal tubulopathy and crystalline cast nephropathy: Biochemical and structural features of disease-causing monoclonal kappa light chains.

Ezawa, T., Otomo, R., Kariya, Y., Nozawa, K., Kyoya, S., Furutani, C., Noguchi, K., Yohda, M., Odaka, M., Matsumura, H., Saito, A., Saito, M., Abe, F., Fujioka, Y., Kitadate, A., Wakui, H., Takahashi, N.

(2025) FASEB J 39: e70296-e70296

PubMed: 39781602 Search on PubMed
DOI: https://doi.org/10.1096/fj.202402104R
Primary Citation of Related Structures:
8XWZ

PubMed Abstract:
Various tubular diseases in patients with multiple myeloma (MM) are caused by monoclonal immunoglobulin light chains (LCs). However, the physicochemical characteristics of the disease-causing LCs contributing to the onset of MM-associated tubular diseases remain unclear. We herein report a rare case of MM-associated combined tubulopathies: non-crystalline light chain proximal tubulopathy (LCPT) and crystalline light chain cast nephropathy (LCCN). The patient's urinary κ-LC (Bence-Jones proteins, BJP-κ PT-CN) was detected through immunofixation. Renal biopsy revealed cytoplasmic vacuoles in swollen proximal tubular cells and distal tubular casts. Immunohistochemistry showed proximal tubular reabsorption granules and distal tubular casts positively stained with an anti-κ-LC antibody. Electron microscopy identified vacuolation and an increased number of lysosomes in proximal tubular epithelial cells without crystalline structures. Distal tubular casts comprised numerous crystals with both rod-shaped and needle-like configurations and tube-shaped materials. To elucidate the molecular mechanisms underlying tubular toxicity, we performed the following physicochemical analyses of BJP-κ PT-CN: N-terminal amino acid sequencing, cDNA cloning, size-exclusion chromatography, thermal shift assays, and X-ray crystallography. The variable segment of BJP-κ PT-CN was derived from the IGKV1-39 gene. The characteristic features of BJP-κ PT-CN were a positively charged surface patch, concentration-dependent monomer-dimer equilibrium, and the R61G mutation. This is the first biochemical and structural characterization of disease-causing BJPs in MM-associated LCPT and crystalline LCCN. The results obtained suggest that these characteristic features enhance protein binding to negatively charged sites on brush-border membranes in proximal tubules and promote the formation of organized casts in distal tubular lumens.

Organizational Affiliation

Department of Life Science, Graduate School of Engineering Science, Akita University, Akita, Japan.

Macromolecule Content

Total Structure Weight: 51.9 kDa
Atom Count: 3,733
Modeled Residue Count: 425
Deposited Residue Count: 428
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bence-Jones protein kappa light chain PT-CN	A, B	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain PA [auth B] SDF format, chain QA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B]	PA [auth B], QA [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain PA [auth B] Focus chain QA [auth B] Interactions & Density Focus chain PA [auth B] Focus chain QA [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain NA [auth B] SDF format, chain OA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B]	C [auth A], D [auth A], NA [auth B], OA [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain NA [auth B] Focus chain OA [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain NA [auth B] Focus chain OA [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain RA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain RA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain RA [auth B]	G [auth A], RA [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain RA [auth B] Interactions & Density Focus chain G [auth A] Focus chain RA [auth B]
ETX Query on ETX Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	2-ETHOXYETHANOL C₄ H₁₀ O₂ ZNQVEEAIQZEUHB-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth B] SDF format, chain AC [auth B] SDF format, chain BA [auth A] SDF format, chain BB [auth B] SDF format, chain BC [auth B] SDF format, chain CA [auth A] SDF format, chain CB [auth B] SDF format, chain CC [auth B] SDF format, chain DA [auth A] SDF format, chain DB [auth B] SDF format, chain EA [auth A] SDF format, chain EB [auth B] SDF format, chain FA [auth A] SDF format, chain FB [auth B] SDF format, chain GA [auth A] SDF format, chain GB [auth B] SDF format, chain H [auth A] SDF format, chain HA [auth A] SDF format, chain HB [auth B] SDF format, chain I [auth A] SDF format, chain IA [auth A] SDF format, chain IB [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth A] SDF format, chain JB [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth A] SDF format, chain KB [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth A] SDF format, chain LB [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth A] SDF format, chain MB [auth B] SDF format, chain N [auth A] SDF format, chain NB [auth B] SDF format, chain O [auth A] SDF format, chain OB [auth B] SDF format, chain P [auth A] SDF format, chain PB [auth B] SDF format, chain Q [auth A] SDF format, chain QB [auth B] SDF format, chain R [auth A] SDF format, chain RB [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain SB [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain TB [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain UB [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain VB [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain WB [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain XB [auth B] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain YB [auth B] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] SDF format, chain ZB [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain AC [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain BC [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain CC [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain IB [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain KB [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain MB [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RB [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain SB [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain TB [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain UB [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain VB [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain WB [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain XB [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain YB [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain ZB [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain AC [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain BC [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth B] mmCIF format, chain CC [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth B] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth B] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain IB [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain JB [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain KB [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain LB [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain MB [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NB [auth B] mmCIF format, chain O [auth A] mmCIF format, chain OB [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PB [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QB [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RB [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain SB [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain TB [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain UB [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain VB [auth B] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain WB [auth B] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain XB [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain YB [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth B] mmCIF format, chain ZB [auth B]	AA [auth A] AB [auth B] AC [auth B] BA [auth A] BB [auth B] AA [auth A], AB [auth B], AC [auth B], BA [auth A], BB [auth B], BC [auth B], CA [auth A], CB [auth B], CC [auth B], DA [auth A], DB [auth B], EA [auth A], EB [auth B], FA [auth A], FB [auth B], GA [auth A], GB [auth B], H [auth A], HA [auth A], HB [auth B], I [auth A], IA [auth A], IB [auth B], J [auth A], JA [auth A], JB [auth B], K [auth A], KA [auth A], KB [auth B], L [auth A], LA [auth A], LB [auth B], M [auth A], MA [auth A], MB [auth B], N [auth A], NB [auth B], O [auth A], OB [auth B], P [auth A], PB [auth B], Q [auth A], QB [auth B], R [auth A], RB [auth B], S [auth A], SA [auth B], SB [auth B], T [auth A], TA [auth B], TB [auth B], U [auth A], UA [auth B], UB [auth B], V [auth A], VA [auth B], VB [auth B], W [auth A], WA [auth B], WB [auth B], X [auth A], XA [auth B], XB [auth B], Y [auth A], YA [auth B], YB [auth B], Z [auth A], ZA [auth B], ZB [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain AC [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain BC [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain CC [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain H [auth A] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KA [auth A] Focus chain KB [auth B] Focus chain L [auth A] Focus chain LA [auth A] Focus chain LB [auth B] Focus chain M [auth A] Focus chain MA [auth A] Focus chain MB [auth B] Focus chain N [auth A] Focus chain NB [auth B] Focus chain O [auth A] Focus chain OB [auth B] Focus chain P [auth A] Focus chain PB [auth B] Focus chain Q [auth A] Focus chain QB [auth B] Focus chain R [auth A] Focus chain RB [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XB [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YB [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain AC [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain BC [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain CC [auth B] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain GA [auth A] Focus chain GB [auth B] Focus chain H [auth A] Focus chain HA [auth A] Focus chain HB [auth B] Focus chain I [auth A] Focus chain IA [auth A] Focus chain IB [auth B] Focus chain J [auth A] Focus chain JA [auth A] Focus chain JB [auth B] Focus chain K [auth A] Focus chain KA [auth A] Focus chain KB [auth B] Focus chain L [auth A] Focus chain LA [auth A] Focus chain LB [auth B] Focus chain M [auth A] Focus chain MA [auth A] Focus chain MB [auth B] Focus chain N [auth A] Focus chain NB [auth B] Focus chain O [auth A] Focus chain OB [auth B] Focus chain P [auth A] Focus chain PB [auth B] Focus chain Q [auth A] Focus chain QB [auth B] Focus chain R [auth A] Focus chain RB [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain XB [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain YB [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Focus chain ZB [auth B]