8SW4

BG505 GT1.1 SOSIP in complex with NHP Fabs 21N13, 21M20 and RM20A3

PDB DOI: https://doi.org/10.2210/pdb8SW4/pdb
EM Map EMD-40797: EMDB EMDataResource

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

Deposited: 2023-05-17 Released: 2024-05-29
Deposition Author(s): Ozorowski, G., Torres, J.L., Zhang, S., Ward, A.B.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.85 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

Neutralizing antibodies induced in non-human primates by germline targeting Env trimer

Caniels, T., Ozorowski, G., Ward, A.B., Sanders, R.W.

To be published.

Macromolecule Content

Total Structure Weight: 412.57 kDa
Atom Count: 26,323
Modelled Residue Count: 3,303
Deposited Residue Count: 3,634
Unique protein chains: 8

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
21M20 heavy chain variable region	A [auth H]	125	Macaca	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
21M20 light chain variable region	B [auth L]	107	Macaca	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 GT1.1 SOSIP gp120	C [auth A], G [auth C], K [auth D]	509	Human immunodeficiency virus 1	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	D [auth B], H [auth G], L [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
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RM20A3 heavy chain variable region	E, I [auth J], M [auth K]	124	Macaca	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
RM20A3 light chain variable region	F, J [auth M], N	111	Macaca	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
21N13 heavy chain variable region	O, Q, S	130	Macaca	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
21N13 light chain variable region	P, R, T	107	Macaca	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: 9
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	U, W, X	4		N-Glycosylation	Interactions Focus chain U Focus chain W Focus chain X Interactions & Density Focus chain U Focus chain W Focus chain X
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	V	2		N-Glycosylation	Interactions Focus chain V Interactions & Density Focus chain V
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 AA [auth A] SDF format, chain AB [auth D] SDF format, chain BA [auth A] SDF format, chain BB [auth D] SDF format, chain CA [auth A] SDF format, chain CB [auth D] SDF format, chain DA [auth A] SDF format, chain DB [auth I] SDF format, chain EA [auth A] SDF format, chain EB [auth I] SDF format, chain FA [auth A] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth C] 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 D] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain XA [auth D] SDF format, chain Y [auth A] SDF format, chain YA [auth D] SDF format, chain Z [auth A] SDF format, chain ZA [auth D] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth D] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth D] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth D] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth I] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth I] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth C] 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 D] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth D]	AA [auth A] AB [auth D] BA [auth A] BB [auth D] CA [auth A] AA [auth A], AB [auth D], BA [auth A], BB [auth D], CA [auth A], CB [auth D], DA [auth A], DB [auth I], EA [auth A], EB [auth I], FA [auth A], GA [auth B], HA [auth B], IA [auth B], JA [auth C], 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 D], VA [auth D], WA [auth D], XA [auth D], Y [auth A], YA [auth D], Z [auth A], ZA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth D] Focus chain BA [auth A] Focus chain BB [auth D] Focus chain CA [auth A] Focus chain CB [auth D] Focus chain DA [auth A] Focus chain DB [auth I] Focus chain EA [auth A] Focus chain EB [auth I] Focus chain FA [auth A] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth C] 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 D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain Y [auth A] Focus chain YA [auth D] Focus chain Z [auth A] Focus chain ZA [auth D] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth D] Focus chain BA [auth A] Focus chain BB [auth D] Focus chain CA [auth A] Focus chain CB [auth D] Focus chain DA [auth A] Focus chain DB [auth I] Focus chain EA [auth A] Focus chain EB [auth I] Focus chain FA [auth A] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth C] 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 D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain Y [auth A] Focus chain YA [auth D] Focus chain Z [auth A] Focus chain ZA [auth D]