8JTD

BJOX2000.664 trimer in complex with Fab fragment of broadly neutralizing HIV antibody PGT145

PDB DOI: https://doi.org/10.2210/pdb8JTD/pdb
EM Map EMD-36641: EMDB EMDataResource

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

Deposited: 2023-06-21 Released: 2023-10-25
Deposition Author(s): Chatterjee, A., Chen, C., Lee, K., Mangala Prasad, V.
Funding Organization(s): Bill & Melinda Gates Foundation, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.90 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

An HIV-1 broadly neutralizing antibody overcomes structural and dynamic variation through highly focused epitope targeting.

Hodge, E.A., Chatterjee, A., Chen, C., Naika, G.S., Laohajaratsang, M., Mangala Prasad, V., Lee, K.K.

(2023) Npj Viruses 1

DOI: https://doi.org/10.1038/s44298-023-00002-4

Macromolecule Content

Total Structure Weight: 292.02 kDa
Atom Count: 17,275
Modelled Residue Count: 1,978
Deposited Residue Count: 2,388
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gp120 protein of HIV Envelope trimer	A, C, D	481	Human immunodeficiency virus 1	Mutation(s): 0
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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
gp41 protein of HIV Envelope trimer	B, E, F	153	Human immunodeficiency virus 1	Mutation(s): 0
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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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT145 antibody fragment, heavy chain	G [auth J]	267	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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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT145 antibody fragment, light chain	H [auth N]	219	Homo sapiens	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	AA [auth i], BA [auth j], EA [auth m], FA [auth n], GA [auth o], AA [auth i], BA [auth j], EA [auth m], FA [auth n], GA [auth o], HA [auth p], I [auth O], J [auth P], JA [auth r], K [auth Q], L [auth R], LA [auth u], MA [auth v], NA [auth w], O [auth V], P [auth W], QA [auth z], RA [auth 0], S [auth Z], SA [auth 1], T [auth a], U [auth b], V [auth c], X [auth e], Z [auth h]	2		N-Glycosylation	Interactions Focus chain AA [auth i] Focus chain BA [auth j] Focus chain EA [auth m] Focus chain FA [auth n] Focus chain GA [auth o] Focus chain HA [auth p] Focus chain I [auth O] Focus chain J [auth P] Focus chain JA [auth r] Focus chain K [auth Q] Focus chain L [auth R] Focus chain LA [auth u] Focus chain MA [auth v] Focus chain NA [auth w] Focus chain O [auth V] Focus chain P [auth W] Focus chain QA [auth z] Focus chain RA [auth 0] Focus chain S [auth Z] Focus chain SA [auth 1] Focus chain T [auth a] Focus chain U [auth b] Focus chain V [auth c] Focus chain X [auth e] Focus chain Z [auth h] Interactions & Density Focus chain AA [auth i] Focus chain BA [auth j] Focus chain EA [auth m] Focus chain FA [auth n] Focus chain GA [auth o] Focus chain HA [auth p] Focus chain I [auth O] Focus chain J [auth P] Focus chain JA [auth r] Focus chain K [auth Q] Focus chain L [auth R] Focus chain LA [auth u] Focus chain MA [auth v] Focus chain NA [auth w] Focus chain O [auth V] Focus chain P [auth W] Focus chain QA [auth z] Focus chain RA [auth 0] Focus chain S [auth Z] Focus chain SA [auth 1] Focus chain T [auth a] Focus chain U [auth b] Focus chain V [auth c] Focus chain X [auth e] Focus chain Z [auth h]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
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	DA [auth l], M [auth S], PA [auth y], Q [auth X], W [auth d]	3		N-Glycosylation	Interactions Focus chain DA [auth l] Focus chain M [auth S] Focus chain PA [auth y] Focus chain Q [auth X] Focus chain W [auth d] Interactions & Density Focus chain DA [auth l] Focus chain M [auth S] Focus chain PA [auth y] Focus chain Q [auth X] Focus chain W [auth d]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-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	N [auth T]	6		N-Glycosylation	Interactions Focus chain N [auth T] Interactions & Density Focus chain N [auth T]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 8
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	CA [auth k], OA [auth x], R [auth Y]	5		N-Glycosylation	Interactions Focus chain CA [auth k] Focus chain OA [auth x] Focus chain R [auth Y] Interactions & Density Focus chain CA [auth k] Focus chain OA [auth x] Focus chain R [auth Y]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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	KA [auth s], Y [auth f]	7		N-Glycosylation	Interactions Focus chain KA [auth s] Focus chain Y [auth f] Interactions & Density Focus chain KA [auth s] Focus chain Y [auth f]
Glycosylation Resources
GlyTouCan: G07617FP GlyCosmos: G07617FP GlyGen: G07617FP

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	IA [auth q]	8		N-Glycosylation	Interactions Focus chain IA [auth q] Interactions & Density Focus chain IA [auth q]
Glycosylation Resources
GlyTouCan: G80966KZ GlyCosmos: G80966KZ GlyGen: G80966KZ

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DB [auth C] SDF format, chain EB [auth D] SDF format, chain FB [auth D] SDF format, chain GB [auth D] SDF format, chain HB [auth D] SDF format, chain IB [auth D] SDF format, chain JB [auth E] SDF format, chain KB [auth E] SDF format, chain LB [auth F] SDF format, chain MB [auth F] SDF format, chain TA [auth A] SDF format, chain UA [auth A] SDF format, chain VA [auth A] SDF format, chain WA [auth A] SDF format, chain XA [auth B] SDF format, chain YA [auth B] SDF format, chain ZA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DB [auth C] MOL2 format, chain EB [auth D] MOL2 format, chain FB [auth D] MOL2 format, chain GB [auth D] MOL2 format, chain HB [auth D] MOL2 format, chain IB [auth D] MOL2 format, chain JB [auth E] MOL2 format, chain KB [auth E] MOL2 format, chain LB [auth F] MOL2 format, chain MB [auth F] MOL2 format, chain TA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain YA [auth B] MOL2 format, chain ZA [auth B]	AB [auth C] BB [auth C] CB [auth C] DB [auth C] EB [auth D] AB [auth C], BB [auth C], CB [auth C], DB [auth C], EB [auth D], FB [auth D], GB [auth D], HB [auth D], IB [auth D], JB [auth E], KB [auth E], LB [auth F], MB [auth F], TA [auth A], UA [auth A], VA [auth A], WA [auth A], XA [auth B], YA [auth B], ZA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain JB [auth E] Focus chain KB [auth E] Focus chain LB [auth F] Focus chain MB [auth F] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EB [auth D] Focus chain FB [auth D] Focus chain GB [auth D] Focus chain HB [auth D] Focus chain IB [auth D] Focus chain JB [auth E] Focus chain KB [auth E] Focus chain LB [auth F] Focus chain MB [auth F] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth B] Focus chain YA [auth B] Focus chain ZA [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:
RECONSTRUCTION	RELION

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2023-10-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1126258
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI140868
Other government	India	--

Revision History (Full details and data files)

Version 1.0: 2023-10-25
Type: Initial release

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Help and Resources

8JTD

BJOX2000.664 trimer in complex with Fab fragment of broadly neutralizing HIV antibody PGT145

An HIV-1 broadly neutralizing antibody overcomes structural and dynamic variation through highly focused epitope targeting.

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

Entity ID: 9

Glycosylation Resources

Entity ID: 10

Glycosylation Resources

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)