9D3D

Cryo-EM structure of PGT145 R100aS Fab bound to HIV-1 BG505 DS-SOSIP.664 Env trimer

PDB DOI: https://doi.org/10.2210/pdb9D3D/pdb
EM Map EMD-46532: EMDB EMDataResource

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

Deposited: 2024-08-09 Released: 2024-12-25
Deposition Author(s): Hodges, S., Morano, N.C., Shapiro, L., Kwong, P.D., Gorman, J.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.41 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

Structural Development of the HIV-1 Apex-Directed PGT145-PGDM1400 Antibody Lineage

Hodges, S., Gorman, J.

(2024) Cell Rep

Macromolecule Content

Total Structure Weight: 290.01 kDa
Atom Count: 17,243
Modelled Residue Count: 1,973
Deposited Residue Count: 2,365
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 BG505 DS-SOSIP gp120	A [auth C], B [auth A], C [auth B]	481	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 18	Glycosylation Focus chain A [auth C] Focus chain B [auth A] Focus chain C [auth B]
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BG505 DS-SOSIP glycoprotein gp41	D [auth c], E [auth a], F [auth b]	153	Human immunodeficiency virus 1	Mutation(s): 2 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain D [auth c] Focus chain E [auth a] Focus chain F [auth b]
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT145 R100aS Heavy Chain	G [auth H]	244	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
PGT145 Light Chain	H [auth L]	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 X], CA [auth Z], DA [auth d], EA [auth e], FA [auth f], AA [auth X], CA [auth Z], DA [auth d], EA [auth e], FA [auth f], GA [auth g], I [auth D], IA [auth i], J [auth E], JA [auth j], K [auth F], KA [auth k], N [auth J], NA [auth n], O [auth K], OA [auth o], Q [auth N], R [auth O], V [auth S], W [auth T], X [auth U], Y [auth V]	2		N-Glycosylation	Interactions Focus chain AA [auth X] Focus chain CA [auth Z] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain I [auth D] Focus chain IA [auth i] Focus chain J [auth E] Focus chain JA [auth j] Focus chain K [auth F] Focus chain KA [auth k] Focus chain N [auth J] Focus chain NA [auth n] Focus chain O [auth K] Focus chain OA [auth o] Focus chain Q [auth N] Focus chain R [auth O] Focus chain V [auth S] Focus chain W [auth T] Focus chain X [auth U] Focus chain Y [auth V] Interactions & Density Focus chain AA [auth X] Focus chain CA [auth Z] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain I [auth D] Focus chain IA [auth i] Focus chain J [auth E] Focus chain JA [auth j] Focus chain K [auth F] Focus chain KA [auth k] Focus chain N [auth J] Focus chain NA [auth n] Focus chain O [auth K] Focus chain OA [auth o] Focus chain Q [auth N] Focus chain R [auth O] Focus chain V [auth S] Focus chain W [auth T] Focus chain X [auth U] Focus chain Y [auth V]
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	HA [auth h], L [auth G]	5		N-Glycosylation	Interactions Focus chain HA [auth h] Focus chain L [auth G] Interactions & Density Focus chain HA [auth h] Focus chain L [auth G]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 7
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	LA [auth l], M [auth I]	4		N-Glycosylation	Interactions Focus chain LA [auth l] Focus chain M [auth I] Interactions & Density Focus chain LA [auth l] Focus chain M [auth I]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 8
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	BA [auth Y], P [auth M], QA [auth q], T [auth Q], Z [auth W]	3		N-Glycosylation	Interactions Focus chain BA [auth Y] Focus chain P [auth M] Focus chain QA [auth q] Focus chain T [auth Q] Focus chain Z [auth W] Interactions & Density Focus chain BA [auth Y] Focus chain P [auth M] Focus chain QA [auth q] Focus chain T [auth Q] Focus chain Z [auth W]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	PA [auth p], RA [auth r], S [auth P]	6		N-Glycosylation	Interactions Focus chain PA [auth p] Focus chain RA [auth r] Focus chain S [auth P] Interactions & Density Focus chain PA [auth p] Focus chain RA [auth r] Focus chain S [auth P]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

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)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	U [auth R]	7		N-Glycosylation	Interactions Focus chain U [auth R] Interactions & Density Focus chain U [auth R]
Glycosylation Resources
GlyTouCan: G07617FP GlyCosmos: G07617FP GlyGen: G07617FP

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	MA [auth m]	3		N-Glycosylation	Interactions Focus chain MA [auth m] Interactions & Density Focus chain MA [auth m]
Glycosylation Resources
GlyTouCan: G44266EX GlyCosmos: G44266EX GlyGen: G44266EX

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain CB [auth A] SDF format, chain DB [auth A] SDF format, chain EB [auth A] SDF format, chain GB [auth B] SDF format, chain HB [auth B] SDF format, chain IB [auth B] SDF format, chain KB [auth B] SDF format, chain LB [auth c] SDF format, chain MB [auth c] SDF format, chain NB [auth a] SDF format, chain PB [auth b] SDF format, chain QB [auth b] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth A] SDF format, chain ZA [auth A] SDF format, chain AB [auth A] SDF format, chain BB [auth A] SDF format, chain JB [auth B] SDF format, chain OB [auth a] SDF format, chain VA [auth C] MOL2 format, chain CB [auth A] MOL2 format, chain DB [auth A] MOL2 format, chain EB [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain HB [auth B] MOL2 format, chain IB [auth B] MOL2 format, chain KB [auth B] MOL2 format, chain LB [auth c] MOL2 format, chain MB [auth c] MOL2 format, chain NB [auth a] MOL2 format, chain PB [auth b] MOL2 format, chain QB [auth b] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth A] MOL2 format, chain ZA [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain BB [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain OB [auth a] MOL2 format, chain VA [auth C] mmCIF format, chain CB [auth A] mmCIF format, chain DB [auth A] mmCIF format, chain EB [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain HB [auth B] mmCIF format, chain IB [auth B] mmCIF format, chain KB [auth B] mmCIF format, chain LB [auth c] mmCIF format, chain MB [auth c] mmCIF format, chain NB [auth a] mmCIF format, chain PB [auth b] mmCIF format, chain QB [auth b] mmCIF format, chain SA [auth C] mmCIF format, chain TA [auth C] mmCIF format, chain UA [auth C] mmCIF format, chain WA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain YA [auth A] mmCIF format, chain ZA [auth A] mmCIF format, chain AB [auth A] mmCIF format, chain BB [auth A] mmCIF format, chain JB [auth B] mmCIF format, chain OB [auth a] mmCIF format, chain VA [auth C]	AB [auth A] BB [auth A] CB [auth A] DB [auth A] EB [auth A] AB [auth A], BB [auth A], CB [auth A], DB [auth A], EB [auth A], GB [auth B], HB [auth B], IB [auth B], JB [auth B], KB [auth B], LB [auth c], MB [auth c], NB [auth a], OB [auth a], PB [auth b], QB [auth b], SA [auth C], TA [auth C], UA [auth C], VA [auth C], WA [auth C], XA [auth C], YA [auth A], ZA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth A] Focus chain BB [auth A] Focus chain CB [auth A] Focus chain DB [auth A] Focus chain EB [auth A] Focus chain GB [auth B] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth c] Focus chain MB [auth c] Focus chain NB [auth a] Focus chain OB [auth a] Focus chain PB [auth b] Focus chain QB [auth b] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth A] Focus chain ZA [auth A] Interactions & Density Focus chain AB [auth A] Focus chain BB [auth A] Focus chain CB [auth A] Focus chain DB [auth A] Focus chain EB [auth A] Focus chain GB [auth B] Focus chain HB [auth B] Focus chain IB [auth B] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth c] Focus chain MB [auth c] Focus chain NB [auth a] Focus chain OB [auth a] Focus chain PB [auth b] Focus chain QB [auth b] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth A] Focus chain ZA [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain FB [auth A] MOL2 format, chain FB [auth A] mmCIF format, chain FB [auth A]	FB [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain FB [auth A] Interactions & Density Focus chain FB [auth A]