9MT2 | pdb_00009mt2

Structure of the Machupo virus glycoprotein complex

PDB DOI: https://doi.org/10.2210/pdb9MT2/pdb
EM Map EMD-48598: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Mammarenavirus machupoense
Expression System: Homo sapiens
Mutation(s): Yes
Membrane Protein: Yes MemProtMD

Deposited: 2025-01-10 Released: 2025-07-16
Deposition Author(s): Mann, C.J., Abraham, J.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structure of the Machupo virus glycoprotein complex

Mann, C.J., Abraham, J.

To be published.

Macromolecule Content

Total Structure Weight: 178.83 kDa
Atom Count: 11,871
Modeled Residue Count: 1,410
Deposited Residue Count: 1,488
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-glycoprotein polyprotein GP complex	A, D, G	58	Mammarenavirus machupoense	Mutation(s): 1 Gene Names: GPC Membrane Entity: Yes
UniProt
Find proteins for Q6IUF7 (Machupo virus) Explore Q6IUF7 Go to UniProtKB: Q6IUF7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6IUF7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-glycoprotein polyprotein GP complex	B, E, H	204	Mammarenavirus machupoense	Mutation(s): 0 Gene Names: GPC Membrane Entity: Yes
UniProt
Find proteins for Q8AZ57 (Machupo virus) Explore Q8AZ57 Go to UniProtKB: Q8AZ57
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8AZ57
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain B Focus chain E Focus chain H
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-glycoprotein polyprotein GP complex	C, F, I	234	Mammarenavirus machupoense	Mutation(s): 0 Gene Names: GPC Membrane Entity: Yes
UniProt
Find proteins for Q6IUF7 (Machupo virus) Explore Q6IUF7 Go to UniProtKB: Q6IUF7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6IUF7
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain C Focus chain F Focus chain I
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth V], K [auth T], L [auth S], N [auth K], P [auth M], J [auth V], K [auth T], L [auth S], N [auth K], P [auth M], R [auth O]	3		N-Glycosylation	Interactions Focus chain J [auth V] Focus chain K [auth T] Focus chain L [auth S] Focus chain N [auth K] Focus chain P [auth M] Focus chain R [auth O] Interactions & Density Focus chain J [auth V] Focus chain K [auth T] Focus chain L [auth S] Focus chain N [auth K] Focus chain P [auth M] Focus chain R [auth O]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth J], O [auth L], Q [auth N]	2		N-Glycosylation	Interactions Focus chain M [auth J] Focus chain O [auth L] Focus chain Q [auth N] Interactions & Density Focus chain M [auth J] Focus chain O [auth L] Focus chain Q [auth N]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain Y [auth E] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain HA [auth I] SDF format, chain GA [auth I] SDF format, chain FA [auth H] SDF format, chain EA [auth H] SDF format, chain BA [auth F] SDF format, chain AA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain HA [auth I] MOL2 format, chain GA [auth I] MOL2 format, chain FA [auth H] MOL2 format, chain EA [auth H] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain HA [auth I] mmCIF format, chain GA [auth I] mmCIF format, chain FA [auth H] mmCIF format, chain EA [auth H] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth F] EA [auth H] FA [auth H] GA [auth I] AA [auth F], BA [auth F], EA [auth H], FA [auth H], GA [auth I], HA [auth I], S [auth B], T [auth B], U [auth C], V [auth C], Y [auth E], Z [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth E] Focus chain Z [auth E]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain JA [auth I] SDF format, chain IA [auth I] SDF format, chain DA [auth F] SDF format, chain CA [auth F] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain JA [auth I] MOL2 format, chain IA [auth I] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth F] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain JA [auth I] mmCIF format, chain IA [auth I] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth F]	CA [auth F] DA [auth F] IA [auth I] JA [auth I] W [auth C] CA [auth F], DA [auth F], IA [auth I], JA [auth I], W [auth C], X [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain DA [auth F] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain CA [auth F] Focus chain DA [auth F] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain W [auth C] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286:

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Mann, C.J.

Abraham, J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	DP5OD023084
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	T32AI700245
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	T32GM144273
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-07-16
Type: Initial release

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 9MT2 | pdb_00009mt2

Structure of the Machupo virus glycoprotein complex

Structure of the Machupo virus glycoprotein complex

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 3

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

9MT2 | pdb_00009mt2