9EVZ | pdb_00009evz

HIV-1 envelope glycoprotein (BG505 gp140 SOSIP.664) trimer in complex with ELC07 broadly neutralizing antibody.

PDB DOI: https://doi.org/10.2210/pdb9EVZ/pdb
EM Map EMD-50020: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-04-02 Released: 2025-04-16
Deposition Author(s): Hope, J., Alguel, Y., Nans, A., Cherepanov, P.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), The Francis Crick Institute, Wellcome Trust, Medical Research Council (MRC, United Kingdom), Cancer Research UK

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.92 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

TITLE: Preservation of memory B cell homeostasis in an individual producing broadly neutralizing antibodies against HIV-1

Griffith, S., Muir, L., Suchanek, O., Hope, J., Pade, C., Gibbons, G., Tuong, K., Fung, A., Touizer, E., Rees-Spear, C., Nans, A., Roustan, C., Alguel, Y., Fink, D., Orkin, C., Deayton, J., Anderson, J., Gupta, R.K., Doores, K.J., Cherepanov, P., McKnight, A., Clatworthy, M., McCoy, L.E.

To be published.

Macromolecule Content

Total Structure Weight: 301.09 kDa
Atom Count: 17,512
Modeled Residue Count: 2,113
Deposited Residue Count: 2,561
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	A, B, D [auth F]	170	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for D0PUM0 (Human immunodeficiency virus type 1) Explore D0PUM0 Go to UniProtKB: D0PUM0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0PUM0
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain D [auth F]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	C, E [auth G], F [auth I]	516	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 16	Glycosylation Focus chain C Focus chain E [auth G] Focus chain F [auth I]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ELC07 heavy chain	G [auth H]	268	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ELC07 light chain	H [auth L]	235	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
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	I [auth q]	3		N-Glycosylation	Interactions Focus chain I [auth q] Interactions & Density Focus chain I [auth q]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth u], K [auth D], L [auth E], M [auth J], N [auth K], J [auth u], K [auth D], L [auth E], M [auth J], N [auth K], O [auth M], P [auth N], Q [auth O], R [auth P], S [auth Q], T [auth R], U [auth S], V [auth T], W [auth U], X [auth V], Y [auth W]	2		N-Glycosylation	Interactions Focus chain J [auth u] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth J] Focus chain N [auth K] Focus chain O [auth M] Focus chain P [auth N] Focus chain Q [auth O] Focus chain R [auth P] Focus chain S [auth Q] Focus chain T [auth R] Focus chain U [auth S] Focus chain V [auth T] Focus chain W [auth U] Focus chain X [auth V] Focus chain Y [auth W] Interactions & Density Focus chain J [auth u] Focus chain K [auth D] Focus chain L [auth E] Focus chain M [auth J] Focus chain N [auth K] Focus chain O [auth M] Focus chain P [auth N] Focus chain Q [auth O] Focus chain R [auth P] Focus chain S [auth Q] Focus chain T [auth R] Focus chain U [auth S] Focus chain V [auth T] Focus chain W [auth U] Focus chain X [auth V] Focus chain Y [auth W]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	Z [auth e]	5		N-Glycosylation	Interactions Focus chain Z [auth e] Interactions & Density Focus chain Z [auth e]
Glycosylation Resources
GlyTouCan: G42227JK GlyCosmos: G42227JK GlyGen: G42227JK

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth j], BA [auth k]	4		N-Glycosylation	Interactions Focus chain AA [auth j] Focus chain BA [auth k] Interactions & Density Focus chain AA [auth j] Focus chain BA [auth k]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AB [auth I] SDF format, chain BB [auth I] SDF format, chain CA [auth C] SDF format, chain CB [auth I] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth C] SDF format, chain LA [auth F] SDF format, chain MA [auth G] SDF format, chain NA [auth G] SDF format, chain OA [auth G] SDF format, chain PA [auth G] SDF format, chain QA [auth G] SDF format, chain RA [auth G] SDF format, chain SA [auth G] SDF format, chain TA [auth G] SDF format, chain UA [auth G] SDF format, chain VA [auth G] SDF format, chain WA [auth I] SDF format, chain XA [auth I] SDF format, chain YA [auth I] SDF format, chain ZA [auth I] MOL2 format, chain AB [auth I] MOL2 format, chain BB [auth I] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth I] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth F] MOL2 format, chain MA [auth G] MOL2 format, chain NA [auth G] MOL2 format, chain OA [auth G] MOL2 format, chain PA [auth G] MOL2 format, chain QA [auth G] MOL2 format, chain RA [auth G] MOL2 format, chain SA [auth G] MOL2 format, chain TA [auth G] MOL2 format, chain UA [auth G] MOL2 format, chain VA [auth G] MOL2 format, chain WA [auth I] MOL2 format, chain XA [auth I] MOL2 format, chain YA [auth I] MOL2 format, chain ZA [auth I] mmCIF format, chain AB [auth I] mmCIF format, chain BB [auth I] mmCIF format, chain CA [auth C] mmCIF format, chain CB [auth I] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth F] mmCIF format, chain MA [auth G] mmCIF format, chain NA [auth G] mmCIF format, chain OA [auth G] mmCIF format, chain PA [auth G] mmCIF format, chain QA [auth G] mmCIF format, chain RA [auth G] mmCIF format, chain SA [auth G] mmCIF format, chain TA [auth G] mmCIF format, chain UA [auth G] mmCIF format, chain VA [auth G] mmCIF format, chain WA [auth I] mmCIF format, chain XA [auth I] mmCIF format, chain YA [auth I] mmCIF format, chain ZA [auth I]	AB [auth I] BB [auth I] CA [auth C] CB [auth I] DA [auth C] AB [auth I], BB [auth I], CA [auth C], CB [auth I], DA [auth C], EA [auth C], FA [auth C], GA [auth C], HA [auth C], IA [auth C], JA [auth C], KA [auth C], LA [auth F], MA [auth G], NA [auth G], OA [auth G], PA [auth G], QA [auth G], RA [auth G], SA [auth G], TA [auth G], UA [auth G], VA [auth G], WA [auth I], XA [auth I], YA [auth I], ZA [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth I] Focus chain BB [auth I] Focus chain CA [auth C] Focus chain CB [auth I] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth F] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain PA [auth G] Focus chain QA [auth G] Focus chain RA [auth G] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain WA [auth I] Focus chain XA [auth I] Focus chain YA [auth I] Focus chain ZA [auth I] Interactions & Density Focus chain AB [auth I] Focus chain BB [auth I] Focus chain CA [auth C] Focus chain CB [auth I] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth C] Focus chain LA [auth F] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain PA [auth G] Focus chain QA [auth G] Focus chain RA [auth G] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain WA [auth I] Focus chain XA [auth I] Focus chain YA [auth I] Focus chain ZA [auth I]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.92 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U54AI170791
The Francis Crick Institute	United Kingdom	CC2058
Wellcome Trust	United Kingdom	CC2058
Medical Research Council (MRC, United Kingdom)	United Kingdom	CC2058
Cancer Research UK	United Kingdom	CC2058