9NHJ | pdb_00009nhj

AMC016 v4.2 in complex with FP-A pAb from animal RQk18 at week 43


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Immunofocusing on the conserved fusion peptide of HIV envelope glycoprotein in rhesus macaques.

Pratap, P.P.Cottrell, C.A.Quinn, J.Carnathan, D.G.Bader, D.L.V.Tran, A.S.Enemuo, C.A.Ngo, J.T.Richey, S.T.Gao, H.Shen, X.Greene, K.M.Hurtado, J.Michaels, K.K.Ben-Akiva, E.Lemnios, A.Melo, M.B.Allen, J.D.Ozorowski, G.Crispin, M.Briney, B.Montefiori, D.Silvestri, G.Irvine, D.J.Crotty, S.Ward, A.B.

(2025) NPJ Vaccines 10: 200-200

  • DOI: https://doi.org/10.1038/s41541-025-01252-4
  • Primary Citation of Related Structures:  
    9NHH, 9NHI, 9NHJ, 9NHK, 9NHL, 9NHM, 9NHN, 9NHO, 9NI9

  • PubMed Abstract: 

    During infection, the fusion peptide (FP) of HIV envelope glycoprotein (Env) serves a central role in viral fusion with the host cell. As such, the FP is highly conserved and therefore an attractive epitope for vaccine design. Here, we describe a vaccination study in non-human primates (NHPs) where glycan deletions were made on soluble HIV Env to increase FP epitope exposure. When delivered via implantable osmotic pumps, this immunogen primed immune responses against the FP, which were then boosted with heterologous trimers resulting in a focused immune response targeting the conserved FP epitope. Although autologous immunizations did not elicit high affinity FP-targeting antibodies, the conserved FP epitope on a heterologous trimer further matured the lower affinity, FP-targeting B cells. This study suggests using epitope conservation strategies on distinct Env trimer immunogens can focus humoral responses on desired neutralizing epitopes and suppress immune-distracting antibody responses against non-neutralizing epitopes.


  • Organizational Affiliation
    • Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RQk-FP-A pAb heavy chainA [auth H]124Macaca mulattaMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RQk-FP-A pAb light chainB [auth L]105Macaca mulattaMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
AMC016 v4.2 envelope glycoprotein gp120C [auth A],
E [auth C],
F [auth D]
521Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for E3VMX3 (Human immunodeficiency virus type 1)
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Go to UniProtKB:  E3VMX3
Entity Groups  
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UniProt GroupE3VMX3
Glycosylation
Glycosylation Sites: 11
Sequence Annotations
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AMC016 v4.2 transmembrane protein gp41D [auth G],
G [auth E],
H [auth F]
153Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for C4MJI6 (Human immunodeficiency virus type 1)
Explore C4MJI6 
Go to UniProtKB:  C4MJI6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4MJI6
Glycosylation
Glycosylation Sites: 5
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I [auth B],
L [auth K],
M,
N,
O,
I [auth B],
L [auth K],
M,
N,
O,
Q,
R
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 6
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseJ [auth I],
P,
S
5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Entity ID: 7
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth J]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth D]
BA [auth A]
BB [auth D]
CA [auth C]
AA [auth A],
AB [auth D],
BA [auth A],
BB [auth D],
CA [auth C],
CB [auth D],
DA [auth C],
DB [auth D],
EA [auth C],
EB [auth E],
FA [auth C],
FB [auth E],
GA [auth C],
GB [auth E],
HA [auth C],
HB [auth E],
IA [auth C],
IB [auth E],
JA [auth C],
JB [auth F],
KA [auth C],
KB [auth F],
LA [auth C],
MA [auth C],
NA [auth C],
OA [auth C],
PA [auth D],
QA [auth D],
RA [auth D],
SA [auth D],
T [auth A],
TA [auth D],
U [auth A],
UA [auth D],
V [auth A],
VA [auth D],
W [auth A],
WA [auth D],
X [auth A],
XA [auth D],
Y [auth A],
YA [auth D],
Z [auth A],
ZA [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI145629

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Data collection, Database references