5A7X

negative stain EM of BG505 SOSIP.664 in complex with sCD4, 17b, and 8ANC195

PDB DOI: https://doi.org/10.2210/pdb5A7X/pdb
EM Map EMD-3086: EMDB EMDataResource

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

Deposited: 2015-07-10 Released: 2015-08-05
Deposition Author(s): Scharf, L., Wang, H., Gao, H., Chen, S., McDowall, A., Bjorkman, P.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 17.0 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 467.01 kDa
Atom Count: 31,872
Modelled Residue Count: 4,104
Deposited Residue Count: 4,188
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 YU2 GP120	A, E, I	313	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P35961 (Human immunodeficiency virus type 1 group M subtype B (isolate YU-2)) Explore P35961 Go to UniProtKB: P35961
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35961
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T-CELL SURFACE GLYCOPROTEIN CD4	B, F, J	181	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01730 (Homo sapiens) Explore P01730 Go to UniProtKB: P01730
PHAROS: P01730 GTEx: ENSG00000010610
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01730
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB OF BROADLY NEUTRALIZING ANTIBODY 17B	C, G, K	214	Homo sapiens	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
FAB OF BROADLY NEUTRALIZING ANTIBODY 17B	D, H, L	229	Homo sapiens	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195	M, O, Q	215	Homo sapiens	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: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB OF BROADLY NEUTRALIZING ANTIBODY 8ANC195	N, P, R	244	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 17.0 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	EMAN	2
RECONSTRUCTION	RELION

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2015-08-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-08-05
Type: Initial release
Version 1.1: 2016-08-10
Changes: Database references
Version 2.0: 2017-08-30
Changes: Advisory, Atomic model, Data collection
Version 2.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary