4Z77 | pdb_00004z77

Weak TCR binding to an unstable insulin epitope drives type 1 diabetes

PDB DOI: https://doi.org/10.2210/pdb4Z77/pdb

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

Deposited: 2015-04-06 Released: 2015-06-24
Deposition Author(s): Rizkallah, P.J., Cole, D.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.253 (Depositor), 0.256 (DCC)
R-Value Work:
0.206 (Depositor), 0.212 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Weak TCR binding to an unstable insulin epitope drives type 1 diabetes

Rizkallah, P.J., Cole, D.K.

To be published.

Macromolecule Content

Total Structure Weight: 97.12 kDa
Atom Count: 6,964
Modeled Residue Count: 772
Deposited Residue Count: 772
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, K-D alpha chain	A, D	277	Mus musculus	Mutation(s): 0 Gene Names: H2-K1, H2-K
UniProt
Find proteins for P01902 (Mus musculus) Explore P01902 Go to UniProtKB: P01902
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01902
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, E	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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin	C, F	9	Homo sapiens	Mutation(s): 1 Gene Names: INS
UniProt & NIH Common Fund Data Resources
Find proteins for P01308 (Homo sapiens) Explore P01308 Go to UniProtKB: P01308
PHAROS: P01308 GTEx: ENSG00000254647
Entity Groups
UniProt Group	P01308
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
15P Query on 15P Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain I [auth A] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain I [auth A] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain I [auth A]	I [auth A], W [auth D], X [auth D]	POLYETHYLENE GLYCOL (N=34) C₆₉ H₁₄₀ O₃₅ VUYXVWGKCKTUMF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain I [auth A] Focus chain W [auth D] Focus chain X [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain HA [auth E] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain GA [auth E] SDF format, chain BA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain GA [auth E] MOL2 format, chain BA [auth D] mmCIF format, chain FA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain GA [auth E] mmCIF format, chain BA [auth D]	BA [auth D] FA [auth E] GA [auth E] HA [auth E] M [auth A] BA [auth D], FA [auth E], GA [auth E], HA [auth E], M [auth A], N [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth D] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain M [auth A] Focus chain N [auth A] Interactions & Density Focus chain BA [auth D] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain M [auth A] Focus chain N [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain P [auth B] MOL2 format, chain CA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain P [auth B] mmCIF format, chain CA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain P [auth B]	CA [auth E] G [auth A] H [auth A] O [auth B] P [auth B] CA [auth E], G [auth A], H [auth A], O [auth B], P [auth B], U [auth D], V [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain CA [auth E] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth D] Focus chain V [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain T [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain T [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain T [auth C]	AA [auth D] DA [auth E] EA [auth E] J [auth A] K [auth A] AA [auth D], DA [auth E], EA [auth E], J [auth A], K [auth A], L [auth A], Q [auth B], R [auth B], S [auth B], T [auth C], Y [auth D], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.253 (Depositor), 0.256 (DCC)
R-Value Work: 0.206 (Depositor), 0.212 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.15	α = 90
b = 84.53	β = 106.86
c = 72.86	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-06-24

Deposition Author(s):

Rizkallah, P.J.

Cole, D.K.

Revision History (Full details and data files)

Version 1.0: 2015-06-24
Type: Initial release
Version 1.1: 2024-11-20
Changes: Data collection, Database references, Refinement description, Structure summary