8DOW

Cryo-EM structure of HIV-1 Env(CH848 10.17 DS.SOSIP_DT) in complex with DH1030.1 Fab

PDB DOI: https://doi.org/10.2210/pdb8DOW/pdb
EM Map EMD-27624: EMDB EMDataResource

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

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: 3.69 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

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., Henderson, R.C., Edwards, R.J., Wiehe, K., Saunders, K., Acharya, P., Williams, W., Haynes, B.F.

To be published.

Macromolecule Content

Total Structure Weight: 370.8 kDa
Atom Count: 25,053
Modelled Residue Count: 3,108
Deposited Residue Count: 3,219
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 gp120	A, E, I	463	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for A0A1W6IPB2 (Human immunodeficiency virus 1) Explore A0A1W6IPB2 Go to UniProtKB: A0A1W6IPB2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1W6IPB2
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 gp41	B, F, J	161	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S7 (Human immunodeficiency virus 1) Explore Q2N0S7 Go to UniProtKB: Q2N0S7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DH1030.1 Fab Heavy chain	C, G, K	230	Macaca mulatta	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
DH1030.1 Fab Light Chain	D, H, L	219	Macaca mulatta	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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M, P, Q, R, T M, P, Q, R, T, U, X, Y, Z	2		N-Glycosylation	Interactions Focus chain M Focus chain P Focus chain Q Focus chain R Focus chain T Focus chain U Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain M Focus chain P Focus chain Q Focus chain R Focus chain T Focus chain U Focus chain X Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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	N, S, W	6		N-Glycosylation	Interactions Focus chain N Focus chain S Focus chain W Interactions & Density Focus chain N Focus chain S Focus chain W
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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], O, V	4		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain O Focus chain V Interactions & Density Focus chain AA [auth a] Focus chain O Focus chain V
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 8
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	BA [auth b]	3		N-Glycosylation	Interactions Focus chain BA [auth b] Interactions & Density Focus chain BA [auth b]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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 CA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain LA [auth E] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain OA [auth I] SDF format, chain PA [auth I] SDF format, chain QA [auth I] SDF format, chain RA [auth I] SDF format, chain SA [auth I] SDF format, chain TA [auth I] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain LA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain OA [auth I] MOL2 format, chain PA [auth I] MOL2 format, chain QA [auth I] MOL2 format, chain RA [auth I] MOL2 format, chain SA [auth I] MOL2 format, chain TA [auth I]	CA [auth A] DA [auth A] EA [auth A] FA [auth A] GA [auth A] CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A], IA [auth E], JA [auth E], KA [auth E], LA [auth E], MA [auth E], NA [auth E], OA [auth I], PA [auth I], QA [auth I], RA [auth I], SA [auth I], TA [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth I] Focus chain PA [auth I] Focus chain QA [auth I] Focus chain RA [auth I] Focus chain SA [auth I] Focus chain TA [auth I] Interactions & Density Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth I] Focus chain PA [auth I] Focus chain QA [auth I] Focus chain RA [auth I] Focus chain SA [auth I] Focus chain TA [auth I]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.69 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	ISOLDE
MODEL REFINEMENT	UCSF ChimeraX

Structure Validation

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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

Prepare Data

Validate Data

Deposit Data

Help and Resources

8DOW

Cryo-EM structure of HIV-1 Env(CH848 10.17 DS.SOSIP_DT) in complex with DH1030.1 Fab

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

Entity Groups

Sequence Annotations

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Entity ID: 4

Entity Groups

Sequence Annotations

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Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)