7TCN | pdb_00007tcn

Cryo-EM structure of CH235.12 in complex with HIV-1 Env trimer CH505TF.N279K.SOSIP.664 with high-mannose glycans

PDB DOI: https://doi.org/10.2210/pdb7TCN/pdb
EM Map EMD-25814: EMDB EMDataResource

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

Deposited: 2021-12-27 Released: 2023-08-02
Deposition Author(s): Manne, K., Henderson, R., Acharya, P.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of CH235.12 in complex with HIV-1 Env trimer CH505TF.N279K.G458Y.SOSIP.664

Manne, K.

To be published.

Macromolecule Content

Total Structure Weight: 371.15 kDa
Atom Count: 23,747
Modeled Residue Count: 2,961
Deposited Residue Count: 3,252
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	A, E, I	486	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for M4M0W3 (Human immunodeficiency virus type 1) Explore M4M0W3 Go to UniProtKB: M4M0W3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	M4M0W3
Glycosylation
Glycosylation Sites: 5	Glycosylation Focus chain A Focus chain E Focus chain I
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein 41	B, F, J	160	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus type 1) Explore Q2N0S5 Go to UniProtKB: Q2N0S5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2N0S5
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CH235.12 Fab Heavy Chain	C, G, K	225	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
CH235.12 Fab Light Chain	D, H, L	213	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
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth 0], O [auth M], P [auth N], R [auth e], T [auth j], M [auth 0], O [auth M], P [auth N], R [auth e], T [auth j], V [auth v]	3		N-Glycosylation	Interactions Focus chain M [auth 0] Focus chain O [auth M] Focus chain P [auth N] Focus chain R [auth e] Focus chain T [auth j] Focus chain V [auth v] Interactions & Density Focus chain M [auth 0] Focus chain O [auth M] Focus chain P [auth N] Focus chain R [auth e] Focus chain T [auth j] Focus chain V [auth v]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 6
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	N [auth 4], Q [auth R], U [auth n]	4		N-Glycosylation	Interactions Focus chain N [auth 4] Focus chain Q [auth R] Focus chain U [auth n] Interactions & Density Focus chain N [auth 4] Focus chain Q [auth R] Focus chain U [auth n]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	S [auth h], W [auth y]	2		N-Glycosylation	Interactions Focus chain S [auth h] Focus chain W [auth y] Interactions & Density Focus chain S [auth h] Focus chain W [auth y]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 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 Z [auth A] SDF format, chain Y [auth A] SDF format, chain X [auth A] SDF format, chain LA [auth I] SDF format, chain KA [auth I] SDF format, chain JA [auth I] SDF format, chain IA [auth I] SDF format, chain GA [auth E] SDF format, chain FA [auth E] SDF format, chain EA [auth E] SDF format, chain DA [auth E] SDF format, chain BA [auth A] SDF format, chain AA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain LA [auth I] MOL2 format, chain KA [auth I] MOL2 format, chain JA [auth I] MOL2 format, chain IA [auth I] MOL2 format, chain GA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain BA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain LA [auth I] mmCIF format, chain KA [auth I] mmCIF format, chain JA [auth I] mmCIF format, chain IA [auth I] mmCIF format, chain GA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain BA [auth A] mmCIF format, chain AA [auth A]	AA [auth A] BA [auth A] DA [auth E] EA [auth E] FA [auth E] AA [auth A], BA [auth A], DA [auth E], EA [auth E], FA [auth E], GA [auth E], IA [auth I], JA [auth I], KA [auth I], LA [auth I], X [auth A], Y [auth A], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain LA [auth I] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain LA [auth I] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
MAN (Subject of Investigation/LOI) Query on MAN Download Ideal Coordinates CCD File SDF format, chain MA [auth K] SDF format, chain HA [auth G] SDF format, chain CA [auth C] MOL2 format, chain MA [auth K] MOL2 format, chain HA [auth G] MOL2 format, chain CA [auth C] mmCIF format, chain MA [auth K] mmCIF format, chain HA [auth G] mmCIF format, chain CA [auth C]	CA [auth C], HA [auth G], MA [auth K]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain CA [auth C] Focus chain HA [auth G] Focus chain MA [auth K] Interactions & Density Focus chain CA [auth C] Focus chain HA [auth G] Focus chain MA [auth K]