6V80 | pdb_00006v80

Crystal structure of human CD1d presenting alpha-Galactosylceramide in complex with NKT12 TCR and VHH nanobody 1D12

PDB DOI: https://doi.org/10.2210/pdb6V80/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Lama glama
Expression System: Trichoplusia ni, Escherichia coli BL21(DE3), Escherichia coli
Mutation(s): No

Deposited: 2019-12-10 Released: 2020-09-16
Deposition Author(s): Shahine, A., Rossjohn, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.53 Å
R-Value Free:
0.254 (Depositor), 0.251 (DCC)
R-Value Work:
0.195 (Depositor), 0.209 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

A single-domain bispecific antibody targeting CD1d and the NKT T-cell receptor induces a potent antitumor response.

Shahine, A., Rossjohn, J.

(2020) Nat Cancer

DOI: https://doi.org/10.1038/s43018-020-00111-6

Macromolecule Content

Total Structure Weight: 233.23 kDa
Atom Count: 14,208
Modeled Residue Count: 1,827
Deposited Residue Count: 2,034
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d	A, F	347	Homo sapiens	Mutation(s): 0 Gene Names: CD1D
UniProt & NIH Common Fund Data Resources
Find proteins for P15813 (Homo sapiens) Explore P15813 Go to UniProtKB: P15813
PHAROS: P15813 GTEx: ENSG00000158473
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15813
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain F	Go to GlyGen: P15813-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, G	100	Homo sapiens	Mutation(s): 0 Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
PHAROS: P61769 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor alpha variable 10, nkt tcr alpha chain fusion	C, H	210	Homo sapiens	Mutation(s): 0 Gene Names: TRAV10, B2M, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0B4J240 (Homo sapiens) Explore A0A0B4J240 Go to UniProtKB: A0A0B4J240
PHAROS: A0A0B4J240 GTEx: ENSG00000211784
Find proteins for K7N5M3 (Homo sapiens) Explore K7N5M3 Go to UniProtKB: K7N5M3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	K7N5M3 A0A0B4J240
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
nkt tcr beta chain	D, I	241	Homo sapiens	Mutation(s): 0 Gene Names: B2M, HDCMA22P
UniProt
Find proteins for K7N5M4 (Homo sapiens) Explore K7N5M4 Go to UniProtKB: K7N5M4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K7N5M4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody VHH ID12	E, J	119	Lama glama	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K, L	2		N-Glycosylation	Interactions Focus chain K Focus chain L Interactions & Density Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AGH Query on AGH Download:Ideal Coordinates CCD File SDF format, chain N [auth F] SDF format, chain M [auth A] MOL2 format, chain N [auth F] MOL2 format, chain M [auth A] mmCIF format, chain N [auth F] mmCIF format, chain M [auth A]	M [auth A], N [auth F]	N-{(1S,2R,3S)-1-[(ALPHA-D-GALACTOPYRANOSYLOXY)METHYL]-2,3-DIHYDROXYHEPTADECYL}HEXACOSANAMIDE C₅₀ H₉₉ N O₉ VQFKFAKEUMHBLV-BYSUZVQFSA-N		Interactions Focus chain M [auth A] Focus chain N [auth F] Interactions & Density Focus chain M [auth A] Focus chain N [auth F]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth F] SDF format, chain O [auth F] MOL2 format, chain P [auth F] MOL2 format, chain O [auth F] mmCIF format, chain P [auth F] mmCIF format, chain O [auth F]	O [auth F], P [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain O [auth F] Focus chain P [auth F] Interactions & Density Focus chain O [auth F] Focus chain P [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.53 Å
R-Value Free: 0.254 (Depositor), 0.251 (DCC)
R-Value Work: 0.195 (Depositor), 0.209 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 210.667	α = 90
b = 165.25	β = 90
c = 84.497	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2020-09-16

Deposition Author(s):

Shahine, A.

Rossjohn, J.

Revision History (Full details and data files)

Version 1.0: 2020-09-16
Type: Initial release
Version 1.1: 2023-10-11
Changes: Advisory, Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary