8SWV

BG505 Boost2 SOSIP.664 in complex with NHP polyclonal antibody IF1

PDB DOI: https://doi.org/10.2210/pdb8SWV/pdb
EM Map EMD-40822: EMDB EMDataResource

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

Deposited: 2023-05-19 Released: 2024-05-22
Deposition Author(s): Pratap, P.P., Antansijevic, A., Ozorowski, G., 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: 3.37 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

Focusing antibody responses to the fusion peptide in rhesus macaques

Cottrell, C.A., Pratap, P.P., Ward, A.B.

To be published.

Macromolecule Content

Total Structure Weight: 258.6 kDa
Atom Count: 14,870
Modelled Residue Count: 1,853
Deposited Residue Count: 2,234
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Surface protein gp120	A, D [auth E], F	516	Human immunodeficiency virus 1	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane protein gp41	B, C, E [auth D]	153	Human immunodeficiency virus 1	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
IF1 Heavy Chain	G [auth H]	122	Macaca mulatta	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
IF1 Light Chain	H [auth L]	105	Macaca mulatta	Mutation(s): 0
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	I [auth G], K [auth J], M, O	2		N-Glycosylation	Interactions Focus chain I [auth G] Focus chain K [auth J] Focus chain M Focus chain O Interactions & Density Focus chain I [auth G] Focus chain K [auth J] Focus chain M Focus chain O
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)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J [auth I], L [auth K]	5		N-Glycosylation	Interactions Focus chain J [auth I] Focus chain L [auth K] Interactions & Density Focus chain J [auth I] Focus chain L [auth K]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 7
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	N	3		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N
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 AA [auth A] SDF format, chain BA [auth A] SDF format, chain BB [auth F] SDF format, chain CA [auth A] SDF format, chain CB [auth F] SDF format, chain DB [auth F] SDF format, chain EA [auth A] SDF format, chain EB [auth F] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain KA [auth E] SDF format, chain MA [auth E] SDF format, chain NA [auth E] SDF format, chain OA [auth E] SDF format, chain P [auth A] SDF format, chain PA [auth E] SDF format, chain Q [auth A] SDF format, chain QA [auth E] SDF format, chain R [auth A] SDF format, chain RA [auth E] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain W [auth A] SDF format, chain WA [auth D] SDF format, chain X [auth A] SDF format, chain XA [auth D] SDF format, chain Y [auth A] SDF format, chain YA [auth F] SDF format, chain Z [auth A] SDF format, chain ZA [auth F] SDF format, chain AB [auth F] SDF format, chain DA [auth A] SDF format, chain LA [auth E] SDF format, chain SA [auth E] SDF format, chain TA [auth E] SDF format, chain UA [auth E] SDF format, chain V [auth A] SDF format, chain VA [auth D] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth F] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth F] MOL2 format, chain DB [auth F] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth F] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain KA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain NA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth F] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth F] MOL2 format, chain AB [auth F] MOL2 format, chain DA [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain SA [auth E] MOL2 format, chain TA [auth E] MOL2 format, chain UA [auth E] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth D]	AA [auth A] AB [auth F] BA [auth A] BB [auth F] CA [auth A] AA [auth A], AB [auth F], BA [auth A], BB [auth F], CA [auth A], CB [auth F], DA [auth A], DB [auth F], EA [auth A], EB [auth F], FA [auth B], GA [auth B], HA [auth B], IA [auth C], JA [auth C], KA [auth E], LA [auth E], MA [auth E], NA [auth E], OA [auth E], P [auth A], PA [auth E], Q [auth A], QA [auth E], R [auth A], RA [auth E], S [auth A], SA [auth E], T [auth A], TA [auth E], U [auth A], UA [auth E], V [auth A], VA [auth D], W [auth A], WA [auth D], X [auth A], XA [auth D], Y [auth A], YA [auth F], Z [auth A], ZA [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth F] Focus chain BA [auth A] Focus chain BB [auth F] Focus chain CA [auth A] Focus chain CB [auth F] Focus chain DA [auth A] Focus chain DB [auth F] Focus chain EA [auth A] Focus chain EB [auth F] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain R [auth A] Focus chain RA [auth E] Focus chain S [auth A] Focus chain SA [auth E] Focus chain T [auth A] Focus chain TA [auth E] Focus chain U [auth A] Focus chain UA [auth E] Focus chain V [auth A] Focus chain VA [auth D] Focus chain W [auth A] Focus chain WA [auth D] Focus chain X [auth A] Focus chain XA [auth D] Focus chain Y [auth A] Focus chain YA [auth F] Focus chain Z [auth A] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth F] Focus chain BA [auth A] Focus chain BB [auth F] Focus chain CA [auth A] Focus chain CB [auth F] Focus chain DA [auth A] Focus chain DB [auth F] Focus chain EA [auth A] Focus chain EB [auth F] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain KA [auth E] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain R [auth A] Focus chain RA [auth E] Focus chain S [auth A] Focus chain SA [auth E] Focus chain T [auth A] Focus chain TA [auth E] Focus chain U [auth A] Focus chain UA [auth E] Focus chain V [auth A] Focus chain VA [auth D] Focus chain W [auth A] Focus chain WA [auth D] Focus chain X [auth A] Focus chain XA [auth D] Focus chain Y [auth A] Focus chain YA [auth F] Focus chain Z [auth A] Focus chain ZA [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.37 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI136621
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1AI10066
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	UM1 AI144462