4Y2D | pdb_00004y2d

Crystal structure of the mCD1d/7DW8-5/iNKTCR ternary complex

PDB DOI: https://doi.org/10.2210/pdb4Y2D/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Homo sapiens
Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-02-09 Released: 2015-05-27
Deposition Author(s): Zajonc, D.M., Yu, E.D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free:
0.257 (Depositor), 0.255 (DCC)
R-Value Work:
0.217 (Depositor), 0.216 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.2 of the entry. See complete history.

Literature

Structural modifications of alphaGalCer in both lipid and carbohydrate moiety influence activation of murine and human iNKT cells

Birkholz, A., Nemcovic, M., Yu, E.D., Girardi, E., Wang, J., Khurana, A., Pauwels, N., Franck, R.W., Tsuji, M., Howell, A., Calenbergh, S., Kronenberg, M., Zajonc, D.M.

To be published.

Macromolecule Content

Total Structure Weight: 191.93 kDa
Atom Count: 11,943
Modeled Residue Count: 1,559
Deposited Residue Count: 1,668
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen-presenting glycoprotein CD1d1	A, E	285	Mus musculus	Mutation(s): 1 Gene Names: Cd1d1, Cd1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11609 (Mus musculus) Explore P11609 Go to UniProtKB: P11609
IMPC: MGI:107674
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11609
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain E	Go to GlyGen: P11609-1
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, F	99	Mus musculus	Mutation(s): 0 Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus) Explore P01887 Go to UniProtKB: P01887
IMPC: MGI:88127
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01887
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)	C, G	209	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0 Gene Names: Trav11, Trav11d
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0B4J1J9 (Mus musculus) Explore A0A0B4J1J9 Go to UniProtKB: A0A0B4J1J9
Find proteins for P01848 (Homo sapiens) Explore P01848 Go to UniProtKB: P01848
PHAROS: P01848
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P01848 A0A0B4J1J9
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)	D, H	241	Mus musculus, Homo sapiens This entity is chimeric	Mutation(s): 0 Gene Names: TRBC2, TCRBC2
UniProt & NIH Common Fund Data Resources
Find proteins for A0A5B9 (Homo sapiens) Explore A0A5B9 Go to UniProtKB: A0A5B9
PHAROS: A0A5B9
Find proteins for A2NTY6 (Mus musculus) Explore A2NTY6 Go to UniProtKB: A2NTY6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	A0A5B9 A2NTY6
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I	2		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7DW Query on 7DW Download:Ideal Coordinates CCD File SDF format, chain Q [auth E] SDF format, chain M [auth A] MOL2 format, chain Q [auth E] MOL2 format, chain M [auth A] mmCIF format, chain Q [auth E] mmCIF format, chain M [auth A]	M [auth A], Q [auth E]	11-(4-fluorophenyl)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]undecanamide C₄₁ H₇₂ F N O₉ GIXLTJURKGIRDL-IWVUWWQKSA-N		Interactions Focus chain M [auth A] Focus chain Q [auth E] Interactions & Density Focus chain M [auth A] Focus chain Q [auth E]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain O [auth E] SDF format, chain P [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth E] mmCIF format, chain P [auth E]	J [auth A], K [auth A], L [auth A], O [auth E], P [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth E] Focus chain P [auth E] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth E] Focus chain P [auth E]
FUC Query on FUC Download:Ideal Coordinates CCD File SDF format, chain N [auth E] MOL2 format, chain N [auth E] mmCIF format, chain N [auth E]	N [auth E]	alpha-L-fucopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-SXUWKVJYSA-N		Interactions Focus chain N [auth E] Interactions & Density Focus chain N [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.257 (Depositor), 0.255 (DCC)
R-Value Work: 0.217 (Depositor), 0.216 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.422	α = 90
b = 150.264	β = 96.24
c = 100.8	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-05-27

Deposition Author(s):

Zajonc, D.M.

Yu, E.D.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI074952

Revision History (Full details and data files)

Version 1.0: 2015-05-27
Type: Initial release
Version 1.1: 2017-09-13
Changes: Author supporting evidence, Derived calculations, Source and taxonomy
Version 2.0: 2017-11-29
Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Refinement description, Structure summary
Version 2.1: 2019-12-11
Changes: Author supporting evidence, Data collection
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 3.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary
Version 3.2: 2024-11-06
Changes: Structure summary