7Z5Q | pdb_00007z5q

Crystal structure of human insulin, crystallised in the presence of macrophage migration inhibitory factor (MIF) and p-Hydroxyphenylpyruvate (HPP)

PDB DOI: https://doi.org/10.2210/pdb7Z5Q/pdb

Classification: HORMONE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-09 Released: 2023-03-22
Deposition Author(s): van den Elsen, J.M.H., Wahid, A.A., Crennell, S.J.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.183 (Depositor), 0.185 (DCC)
R-Value Work:
0.165 (Depositor), 0.166 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Dissociation of Hexameric Insulin Facilitated by Macrophage Migration Inhibitory Factor Indicates a Novel Role in Insulin Signalling

Wahid, A.A., Kasaar, O., Ronsse, D., Smith, K., Hyland, A., Staddon, W., Scrivens, B., Babarinde, S.O., Dunphy, R., Cozier, G.E., Koumanov, F., Crennell, S.J., Williams, R.J., van den Elsen, J.M.H.

To be published.

Macromolecule Content

Total Structure Weight: 5.91 kDa
Atom Count: 478
Modeled Residue Count: 51
Deposited Residue Count: 51
Unique protein chains: 2

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin A chain	A	21	Homo sapiens	Mutation(s): 0 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
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01308
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Insulin	B	30	Homo sapiens	Mutation(s): 0 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
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01308
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.183 (Depositor), 0.185 (DCC)
R-Value Work: 0.165 (Depositor), 0.166 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.939	α = 90
b = 77.939	β = 90
c = 77.939	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
BALBES	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-22

Deposition Author(s):

van den Elsen, J.M.H.

Funding Organization	Location	Grant Number
Other private	United Kingdom	R320/1113

Revision History (Full details and data files)

Version 1.0: 2023-03-22
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.