8DP1 | pdb_00008dp1

Cryo-EM structure of HIV-1 Env(BG505.T332N SOSIP) in complex with DH1030.1 Fab

PDB DOI: https://doi.org/10.2210/pdb8DP1/pdb
EM Map EMD-27628: EMDB EMDataResource

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

Deposited: 2022-07-14 Released: 2023-07-19
Deposition Author(s): Gobeil, S., Acharya, P.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.46 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Shared recognition mechanism for HIV-1 envelope-reactive V3 glycan broadly neutralizing B cell lineage maturation in humans and macaques

Gobeil, S.M., Janowska, K., Stalls, V., Mansouri, K., Edwards, R.J., Henderson, R.C., Wiehe, K., Saunders, K., Acharya, P., Williams, W., Haynes, B.F.

To be published.

Macromolecule Content

Total Structure Weight: 379.35 kDa
Atom Count: 25,000
Modeled Residue Count: 3,045
Deposited Residue Count: 3,249
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DH1030.1 Fab light chain	A [auth M], G [auth F], K [auth O]	219	Macaca mulatta	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DH1030.1 Fab Heavy chain	B [auth R], F [auth E], J [auth N]	230	Macaca mulatta	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	C [auth S], H, L [auth Q]	153	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain C [auth S] Focus chain H Focus chain L [auth Q]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	D [auth W], E [auth B], I [auth J]	481	Human immunodeficiency virus 1	Mutation(s): 2 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 13	Glycosylation Focus chain D [auth W] Focus chain E [auth B] Focus chain I [auth J]
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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-glucopyranose	M [auth A], R [auth K], W [auth V]	10		N-Glycosylation	Interactions Focus chain M [auth A] Focus chain R [auth K] Focus chain W [auth V] Interactions & Density Focus chain M [auth A] Focus chain R [auth K] Focus chain W [auth V]
Glycosylation Resources
GlyTouCan: G40702WU GlyCosmos: G40702WU GlyGen: G40702WU

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N [auth C], O [auth D], S [auth L], V [auth U], X	3		N-Glycosylation	Interactions Focus chain N [auth C] Focus chain O [auth D] Focus chain S [auth L] Focus chain V [auth U] Focus chain X Interactions & Density Focus chain N [auth C] Focus chain O [auth D] Focus chain S [auth L] Focus chain V [auth U] Focus chain X
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	P [auth G], Q [auth I], T [auth P], U [auth T], Y, P [auth G], Q [auth I], T [auth P], U [auth T], Y, Z	2		N-Glycosylation	Interactions Focus chain P [auth G] Focus chain Q [auth I] Focus chain T [auth P] Focus chain U [auth T] Focus chain Y Focus chain Z Interactions & Density Focus chain P [auth G] Focus chain Q [auth I] Focus chain T [auth P] Focus chain U [auth T] Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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-glucopyranose	AA [auth a]	5		N-Glycosylation	Interactions Focus chain AA [auth a] Interactions & Density Focus chain AA [auth a]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

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 ZA [auth J] SDF format, chain YA [auth J] SDF format, chain XA [auth J] SDF format, chain WA [auth H] SDF format, chain VA [auth H] SDF format, chain UA [auth H] SDF format, chain TA [auth B] SDF format, chain SA [auth B] SDF format, chain RA [auth B] SDF format, chain QA [auth B] SDF format, chain PA [auth B] SDF format, chain OA [auth B] SDF format, chain NA [auth B] SDF format, chain MA [auth B] SDF format, chain LA [auth W] SDF format, chain KA [auth W] SDF format, chain JA [auth W] SDF format, chain IA [auth W] SDF format, chain HB [auth Q] SDF format, chain HA [auth W] SDF format, chain GB [auth Q] SDF format, chain GA [auth W] SDF format, chain FB [auth Q] SDF format, chain FA [auth W] SDF format, chain EB [auth J] SDF format, chain EA [auth W] SDF format, chain DB [auth J] SDF format, chain DA [auth S] SDF format, chain CB [auth J] SDF format, chain CA [auth S] SDF format, chain BB [auth J] SDF format, chain BA [auth S] SDF format, chain AB [auth J] MOL2 format, chain ZA [auth J] MOL2 format, chain YA [auth J] MOL2 format, chain XA [auth J] MOL2 format, chain WA [auth H] MOL2 format, chain VA [auth H] MOL2 format, chain UA [auth H] MOL2 format, chain TA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain LA [auth W] MOL2 format, chain KA [auth W] MOL2 format, chain JA [auth W] MOL2 format, chain IA [auth W] MOL2 format, chain HB [auth Q] MOL2 format, chain HA [auth W] MOL2 format, chain GB [auth Q] MOL2 format, chain GA [auth W] MOL2 format, chain FB [auth Q] MOL2 format, chain FA [auth W] MOL2 format, chain EB [auth J] MOL2 format, chain EA [auth W] MOL2 format, chain DB [auth J] MOL2 format, chain DA [auth S] MOL2 format, chain CB [auth J] MOL2 format, chain CA [auth S] MOL2 format, chain BB [auth J] MOL2 format, chain BA [auth S] MOL2 format, chain AB [auth J] mmCIF format, chain ZA [auth J] mmCIF format, chain YA [auth J] mmCIF format, chain XA [auth J] mmCIF format, chain WA [auth H] mmCIF format, chain VA [auth H] mmCIF format, chain UA [auth H] mmCIF format, chain TA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain MA [auth B] mmCIF format, chain LA [auth W] mmCIF format, chain KA [auth W] mmCIF format, chain JA [auth W] mmCIF format, chain IA [auth W] mmCIF format, chain HB [auth Q] mmCIF format, chain HA [auth W] mmCIF format, chain GB [auth Q] mmCIF format, chain GA [auth W] mmCIF format, chain FB [auth Q] mmCIF format, chain FA [auth W] mmCIF format, chain EB [auth J] mmCIF format, chain EA [auth W] mmCIF format, chain DB [auth J] mmCIF format, chain DA [auth S] mmCIF format, chain CB [auth J] mmCIF format, chain CA [auth S] mmCIF format, chain BB [auth J] mmCIF format, chain BA [auth S] mmCIF format, chain AB [auth J]	AB [auth J] BA [auth S] BB [auth J] CA [auth S] CB [auth J] AB [auth J], BA [auth S], BB [auth J], CA [auth S], CB [auth J], DA [auth S], DB [auth J], EA [auth W], EB [auth J], FA [auth W], FB [auth Q], GA [auth W], GB [auth Q], HA [auth W], HB [auth Q], IA [auth W], JA [auth W], KA [auth W], LA [auth W], MA [auth B], NA [auth B], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth H], VA [auth H], WA [auth H], XA [auth J], YA [auth J], ZA [auth J]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth J] Focus chain BA [auth S] Focus chain BB [auth J] Focus chain CA [auth S] Focus chain CB [auth J] Focus chain DA [auth S] Focus chain DB [auth J] Focus chain EA [auth W] Focus chain EB [auth J] Focus chain FA [auth W] Focus chain FB [auth Q] Focus chain GA [auth W] Focus chain GB [auth Q] Focus chain HA [auth W] Focus chain HB [auth Q] Focus chain IA [auth W] Focus chain JA [auth W] Focus chain KA [auth W] Focus chain LA [auth W] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth H] Focus chain VA [auth H] Focus chain WA [auth H] Focus chain XA [auth J] Focus chain YA [auth J] Focus chain ZA [auth J] Interactions & Density Focus chain AB [auth J] Focus chain BA [auth S] Focus chain BB [auth J] Focus chain CA [auth S] Focus chain CB [auth J] Focus chain DA [auth S] Focus chain DB [auth J] Focus chain EA [auth W] Focus chain EB [auth J] Focus chain FA [auth W] Focus chain FB [auth Q] Focus chain GA [auth W] Focus chain GB [auth Q] Focus chain HA [auth W] Focus chain HB [auth Q] Focus chain IA [auth W] Focus chain JA [auth W] Focus chain KA [auth W] Focus chain LA [auth W] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth H] Focus chain VA [auth H] Focus chain WA [auth H] Focus chain XA [auth J] Focus chain YA [auth J] Focus chain ZA [auth J]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.46 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	ISOLDE
MODEL REFINEMENT	UCSF ChimeraX
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-19

Deposition Author(s):

Gobeil, S.

Acharya, P.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-07-19
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Refinement description, Structure summary
Version 1.2: 2025-05-14
Changes: Data collection