9F02 | pdb_00009f02

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

PDB DOI: https://doi.org/10.2210/pdb9F02/pdb
EM Map EMD-50092: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2024-04-15 Released: 2025-04-23
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: 3.02 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: 410.66 kDa
Atom Count: 24,183
Modeled Residue Count: 2,991
Deposited Residue Count: 3,567
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein gp41	A, D [auth F], E	170	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S8 (Human immunodeficiency virus type 1) Explore Q2N0S8 Go to UniProtKB: Q2N0S8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S8
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 gp160	B [auth C], C [auth G], L [auth N]	516	Human immunodeficiency virus 1	Mutation(s): 26 Gene Names: env
UniProt
Find proteins for Q2N0S8 (Human immunodeficiency virus type 1) Explore Q2N0S8 Go to UniProtKB: Q2N0S8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S8
Glycosylation
Glycosylation Sites: 16	Glycosylation Focus chain B [auth C] Focus chain C [auth G] Focus chain L [auth N]
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	F [auth H], H [auth I], J [auth K]	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	G [auth L], I [auth J], K [auth M]	235	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
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	GA [auth d], IA [auth g], M [auth e]	4		N-Glycosylation	Interactions Focus chain GA [auth d] Focus chain IA [auth g] Focus chain M [auth e] Interactions & Density Focus chain GA [auth d] Focus chain IA [auth g] Focus chain M [auth e]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 6
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	HA [auth f], JA [auth h], N [auth q]	3		N-Glycosylation	Interactions Focus chain HA [auth f] Focus chain JA [auth h] Focus chain N [auth q] Interactions & Density Focus chain HA [auth f] Focus chain JA [auth h] Focus chain N [auth q]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth X], BA [auth Y], CA [auth Z], DA [auth a], EA [auth b], AA [auth X], BA [auth Y], CA [auth Z], DA [auth a], EA [auth b], FA [auth c], O [auth u], P [auth B], Q [auth D], R [auth O], S [auth P], T [auth Q], U [auth R], V [auth S], W [auth T], X [auth U], Y [auth V], Z [auth W]	2		N-Glycosylation	Interactions Focus chain AA [auth X] Focus chain BA [auth Y] Focus chain CA [auth Z] Focus chain DA [auth a] Focus chain EA [auth b] Focus chain FA [auth c] Focus chain O [auth u] Focus chain P [auth B] Focus chain Q [auth D] Focus chain R [auth O] Focus chain S [auth P] Focus chain T [auth Q] Focus chain U [auth R] Focus chain V [auth S] Focus chain W [auth T] Focus chain X [auth U] Focus chain Y [auth V] Focus chain Z [auth W] Interactions & Density Focus chain AA [auth X] Focus chain BA [auth Y] Focus chain CA [auth Z] Focus chain DA [auth a] Focus chain EA [auth b] Focus chain FA [auth c] Focus chain O [auth u] Focus chain P [auth B] Focus chain Q [auth D] Focus chain R [auth O] Focus chain S [auth P] Focus chain T [auth Q] Focus chain U [auth R] Focus chain V [auth S] Focus chain W [auth T] Focus chain X [auth U] Focus chain Y [auth V] Focus chain Z [auth W]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 BB [auth N] SDF format, chain CB [auth N] SDF format, chain DB [auth N] SDF format, chain EB [auth N] SDF format, chain FB [auth N] SDF format, chain GB [auth N] SDF format, chain HB [auth N] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain QA [auth C] SDF format, chain RA [auth C] 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 G] SDF format, chain XA [auth G] SDF format, chain YA [auth G] SDF format, chain ZA [auth G] SDF format, chain AB [auth N] MOL2 format, chain BB [auth N] MOL2 format, chain CB [auth N] MOL2 format, chain DB [auth N] MOL2 format, chain EB [auth N] MOL2 format, chain FB [auth N] MOL2 format, chain GB [auth N] MOL2 format, chain HB [auth N] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] 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 G] MOL2 format, chain XA [auth G] MOL2 format, chain YA [auth G] MOL2 format, chain ZA [auth G] MOL2 format, chain AB [auth N] mmCIF format, chain BB [auth N] mmCIF format, chain CB [auth N] mmCIF format, chain DB [auth N] mmCIF format, chain EB [auth N] mmCIF format, chain FB [auth N] mmCIF format, chain GB [auth N] mmCIF format, chain HB [auth N] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] 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 G] mmCIF format, chain XA [auth G] mmCIF format, chain YA [auth G] mmCIF format, chain ZA [auth G] mmCIF format, chain AB [auth N]	AB [auth N] BB [auth N] CB [auth N] DB [auth N] EB [auth N] AB [auth N], BB [auth N], CB [auth N], DB [auth N], EB [auth N], FB [auth N], GB [auth N], HB [auth N], KA [auth C], LA [auth C], MA [auth C], NA [auth C], OA [auth C], PA [auth C], QA [auth C], RA [auth C], SA [auth G], TA [auth G], UA [auth G], VA [auth G], WA [auth G], XA [auth G], YA [auth G], ZA [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth N] Focus chain BB [auth N] Focus chain CB [auth N] Focus chain DB [auth N] Focus chain EB [auth N] Focus chain FB [auth N] Focus chain GB [auth N] Focus chain HB [auth N] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain YA [auth G] Focus chain ZA [auth G] Interactions & Density Focus chain AB [auth N] Focus chain BB [auth N] Focus chain CB [auth N] Focus chain DB [auth N] Focus chain EB [auth N] Focus chain FB [auth N] Focus chain GB [auth N] Focus chain HB [auth N] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth G] Focus chain TA [auth G] Focus chain UA [auth G] Focus chain VA [auth G] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain YA [auth G] Focus chain ZA [auth G]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.02 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-23

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