6X98

Cryo-EM model of HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 11B fragment antigen binding variable domain

PDB DOI: https://doi.org/10.2210/pdb6X98/pdb
EM Map EMD-22104: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Oryctolagus cuniculus
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2020-06-02 Released: 2021-12-08
Deposition Author(s): Ozorowski, G., Cottrell, C.A., Ward, A.B.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.38 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Limited breadth of anti-HIV Env glycan hole antibodies is further hindered by strain-specific peptide interactions

Ozorowski, G., Cottrell, C.A., de Val, N., Scaringi, N., Polveroni, T.M., Ward, A.B.

To be published.

Macromolecule Content

Total Structure Weight: 390.73 kDa
Atom Count: 19,269
Modelled Residue Count: 2,367
Deposited Residue Count: 3,441
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 HIV-1 Env gp120	A, E [auth C], I [auth G]	516	Human immunodeficiency virus 1	Mutation(s): 6 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 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 A Focus chain E [auth C] Focus chain I [auth G]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 HIV-1 Env gp41	B, F [auth D], J [auth I]	153	Human immunodeficiency virus 1	Mutation(s): 2 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
monoclonal antibody 11B kappa chain	C [auth L], G [auth E], K [auth J]	237	Oryctolagus cuniculus	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
monoclonal antibody 11B fragment antigen binding heavy chain	D [auth H], H [auth F], L [auth K]	241	Oryctolagus cuniculus	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, O, P, Q, S M, O, P, Q, S, T, U, W, X	2		N-Glycosylation	Interactions Focus chain M Focus chain O Focus chain P Focus chain Q Focus chain S Focus chain T Focus chain U Focus chain W Focus chain X Interactions & Density Focus chain M Focus chain O Focus chain P Focus chain Q Focus chain S Focus chain T Focus chain U Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
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	N, R, V	4		N-Glycosylation	Interactions Focus chain N Focus chain R Focus chain V Interactions & Density Focus chain N Focus chain R Focus chain V
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 AA [auth A] SDF format, chain AB [auth G] SDF format, chain BA [auth A] SDF format, chain BB [auth G] SDF format, chain CA [auth A] SDF format, chain CB [auth G] SDF format, chain DA [auth A] SDF format, chain DB [auth G] SDF format, chain EA [auth A] SDF format, chain EB [auth G] SDF format, chain FA [auth A] SDF format, chain FB [auth G] SDF format, chain GA [auth A] SDF format, chain GB [auth G] SDF format, chain HA [auth A] SDF format, chain HB [auth G] SDF format, chain IA [auth A] SDF format, chain JA [auth A] 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 C] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain WA [auth G] SDF format, chain XA [auth G] SDF format, chain Y [auth A] SDF format, chain YA [auth G] SDF format, chain Z [auth A] SDF format, chain ZA [auth G] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth G] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth G] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth G] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth G] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth G] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth G] MOL2 format, chain GA [auth A] MOL2 format, chain GB [auth G] MOL2 format, chain HA [auth A] MOL2 format, chain HB [auth G] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] 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 C] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth G] MOL2 format, chain XA [auth G] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth G] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth G] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth G] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth G] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth G] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth G] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth G] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth G] mmCIF format, chain GA [auth A] mmCIF format, chain GB [auth G] mmCIF format, chain HA [auth A] mmCIF format, chain HB [auth G] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] 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 C] mmCIF format, chain TA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain WA [auth G] mmCIF format, chain XA [auth G] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth G] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth G]	AA [auth A] AB [auth G] BA [auth A] BB [auth G] CA [auth A] AA [auth A], AB [auth G], BA [auth A], BB [auth G], CA [auth A], CB [auth G], DA [auth A], DB [auth G], EA [auth A], EB [auth G], FA [auth A], FB [auth G], GA [auth A], GB [auth G], HA [auth A], HB [auth G], IA [auth A], JA [auth A], 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 C], TA [auth C], UA [auth C], VA [auth C], WA [auth G], XA [auth G], Y [auth A], YA [auth G], Z [auth A], ZA [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth G] Focus chain BA [auth A] Focus chain BB [auth G] Focus chain CA [auth A] Focus chain CB [auth G] Focus chain DA [auth A] Focus chain DB [auth G] Focus chain EA [auth A] Focus chain EB [auth G] Focus chain FA [auth A] Focus chain FB [auth G] Focus chain GA [auth A] Focus chain GB [auth G] Focus chain HA [auth A] Focus chain HB [auth G] Focus chain IA [auth A] Focus chain JA [auth A] 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 C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain Y [auth A] Focus chain YA [auth G] Focus chain Z [auth A] Focus chain ZA [auth G] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth G] Focus chain BA [auth A] Focus chain BB [auth G] Focus chain CA [auth A] Focus chain CB [auth G] Focus chain DA [auth A] Focus chain DB [auth G] Focus chain EA [auth A] Focus chain EB [auth G] Focus chain FA [auth A] Focus chain FB [auth G] Focus chain GA [auth A] Focus chain GB [auth G] Focus chain HA [auth A] Focus chain HB [auth G] Focus chain IA [auth A] Focus chain JA [auth A] 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 C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain Y [auth A] Focus chain YA [auth G] Focus chain Z [auth A] Focus chain ZA [auth G]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.38 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Rosetta	2020.03.61102
RECONSTRUCTION	cryoSPARC	2

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-12-08

Deposition Author(s):

Ozorowski, G.

Cottrell, C.A.

Ward, A.B.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1AI100663
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI144462
Bill & Melinda Gates Foundation	United States	OPP1115782