4F9Z | pdb_00004f9z

Crystal Structure of human ERp27

PDB DOI: https://doi.org/10.2210/pdb4F9Z/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-05-21 Released: 2012-12-05
Deposition Author(s): Kober, F.X., Koelmel, W., Kuper, J., Schindelin, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.217 (Depositor), 0.211 (DCC)
R-Value Work:
0.170 (Depositor), 0.169 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The Crystal Structure of the Protein-Disulfide Isomerase Family Member ERp27 Provides Insights into Its Substrate Binding Capabilities.

Kober, F.X., Koelmel, W., Kuper, J., Drechsler, J., Mais, C., Hermanns, H.M., Schindelin, H.

(2013) J Biological Chem 288: 2029-2039

PubMed: 23192347 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M112.410522
Primary Citation Related Structures:
4F9Z

PubMed Abstract:
About one-third of all cellular proteins pass through the secretory pathway and hence undergo oxidative folding in the endoplasmic reticulum (ER). Protein-disulfide isomerase (PDI) and related members of the PDI family assist in the folding of substrates by catalyzing the oxidation of two cysteines and isomerization of disulfide bonds as well as by acting as chaperones. In this study, we present the crystal structure of ERp27, a redox-inactive member of the PDI family. The structure reveals its substrate-binding cleft, which is homologous to PDI, but is able to adapt in size and hydrophobicity. Isothermal titration calorimetry experiments demonstrate that ERp27 is able to distinguish between folded and unfolded substrates, only interacting with the latter. ERp27 is up-regulated during ER stress, thus presumably allowing it to bind accumulating misfolded substrates and present them to ERp57 for catalysis.

Organizational Affiliation

Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany.

Macromolecule Content

Total Structure Weight: 128.43 kDa
Atom Count: 9,452
Modeled Residue Count: 1,095
Deposited Residue Count: 1,135
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmic reticulum resident protein 27	A [auth D], B [auth A], C [auth B], D [auth C], E	227	Homo sapiens	Mutation(s): 0 Gene Names: C12orf46, ERP27, UNQ781/PRO1575
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DN0 (Homo sapiens) Explore Q96DN0 Go to UniProtKB: Q96DN0
PHAROS: Q96DN0 GTEx: ENSG00000139055
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96DN0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE3 Query on PE3 Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C₂₈ H₅₈ O₁₅ ILLKMACMBHTSHP-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
PE4 Query on PE4 Download:Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₁₆ H₃₄ O₈ PJWQOENWHPEPKI-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain T [auth E] SDF format, chain S [auth E] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth D] SDF format, chain H [auth D] SDF format, chain G [auth D] SDF format, chain F [auth D] MOL2 format, chain T [auth E] MOL2 format, chain S [auth E] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth D] MOL2 format, chain H [auth D] MOL2 format, chain G [auth D] MOL2 format, chain F [auth D] mmCIF format, chain T [auth E] mmCIF format, chain S [auth E] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth D] mmCIF format, chain H [auth D] mmCIF format, chain G [auth D] mmCIF format, chain F [auth D]	F [auth D] G [auth D] H [auth D] I [auth D] J [auth A] F [auth D], G [auth D], H [auth D], I [auth D], J [auth A], K [auth A], L [auth A], N [auth B], O [auth B], Q [auth C], R [auth C], S [auth E], T [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth D] Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth E] Focus chain T [auth E] Interactions & Density Focus chain F [auth D] Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth E] Focus chain T [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.217 (Depositor), 0.211 (DCC)
R-Value Work: 0.170 (Depositor), 0.169 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.832	α = 70.45
b = 68.359	β = 88.16
c = 86.775	γ = 64.96

Software Package:

Software Name	Purpose
MxCuBE	data collection
SHELXS	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-12-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-12-05
Type: Initial release
Version 1.1: 2013-02-06
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations

4F9Z | pdb_00004f9z

Crystal Structure of human ERp27

Literature

The Crystal Structure of the Protein-Disulfide Isomerase Family Member ERp27 Provides Insights into Its Substrate Binding Capabilities.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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