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9wqu

b-b' domain fragment of ER-60 (ERp57) under microgravity

Method: X-RAY DIFFRACTION Dmax: 124.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protein disulfide-isomerase A3

Homo sapiens

UniProt P30101

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 134–376 Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：COUNTER-DIFFUSION；pH 7；293 K；50 mM HEPES-NaOH, pH 7.0, 20% PEG3350, 50 mM Ammonium Sulfate, 100 m M NaCl, 0.04% NaN3 Resolution 1.80 Å R-free 0.263
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 134–376 Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：COUNTER-DIFFUSION；pH 7；293 K；50 mM HEPES-NaOH, pH 7.0, 20% PEG3350, 50 mM Ammonium Sulfate, 100 m M NaCl, 0.04% NaN3 Resolution 1.80 Å R-free 0.263
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 134–376 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：COUNTER-DIFFUSION；pH 7；293 K；50 mM HEPES-NaOH, pH 7.0, 20% PEG3350, 50 mM Ammonium Sulfate, 100 m M NaCl, 0.04% NaN3 Resolution 1.80 Å R-free 0.263

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9WQU Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2ALB NMR structure of the N-terminal domain a of the glycoprotein chaperone ERp57 Deposited 2005-08-05 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 25–137（113 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 0.8-2.5 mM
Resolution not provided
2DMM The solution structure of the second thioredoxin domain of human Protein disulfide-isomerase A3 Deposited 2006-04-22 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 357–485（129 aa） Fragment：thioredoxin domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.3mM thioredoxin domain U-15N,13C; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O | 90% H2O/10% D2O
Resolution not provided
2H8L Crystal structure of the bb' fragment of ERp57 Deposited 2006-06-07 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 134–376（243 aa） Fragment：;bb' fragment ;
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；30% PEG 3350, 0.1M ammonium sulphate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.250
2H8L Crystal structure of the bb' fragment of ERp57 Deposited 2006-06-07 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 134–376（243 aa） Fragment：;bb' fragment ;
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；30% PEG 3350, 0.1M ammonium sulphate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.250
2H8L Crystal structure of the bb' fragment of ERp57 Deposited 2006-06-07 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 134–376（243 aa） Fragment：;bb' fragment ;
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；30% PEG 3350, 0.1M ammonium sulphate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.250
3F8U Tapasin/ERp57 heterodimer Deposited 2008-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 25–505（481 aa）
Mutation：C60A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；reservoir contained 100 mM HEPES (@pH 7.5), 20% PEG 3K, 200 mM CaCl2. protein was concentrated to 10mg/ml in 150 mM NaCl, 20 mM Tris (@ pH 7.4), 5% glycerol. The hanging drop was supplemented to contain 100 mM guanidine HCl; seeding was used to obtain larger crystals., VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.60 Å R-free 0.285
3F8U Tapasin/ERp57 heterodimer Deposited 2008-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 25–505（481 aa）
Mutation：C60A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；reservoir contained 100 mM HEPES (@pH 7.5), 20% PEG 3K, 200 mM CaCl2. protein was concentrated to 10mg/ml in 150 mM NaCl, 20 mM Tris (@ pH 7.4), 5% glycerol. The hanging drop was supplemented to contain 100 mM guanidine HCl; seeding was used to obtain larger crystals., VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.60 Å R-free 0.285
3F8U Tapasin/ERp57 heterodimer Deposited 2008-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 25–505（481 aa）
Chain C 25–505（481 aa）
Mutation：C60A Mutation：C60A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；reservoir contained 100 mM HEPES (@pH 7.5), 20% PEG 3K, 200 mM CaCl2. protein was concentrated to 10mg/ml in 150 mM NaCl, 20 mM Tris (@ pH 7.4), 5% glycerol. The hanging drop was supplemented to contain 100 mM guanidine HCl; seeding was used to obtain larger crystals., VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.60 Å R-free 0.285
6ENY Structure of the human PLC editing module Deposited 2017-10-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 25–505（481 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.80 Å
7QNG Structure of a MHC I-Tapasin-ERp57 complex Deposited 2021-12-20 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–505（505 aa）
Mutation：C60A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；100 mM Gly-Gly, AMPD, pH 8.5, 300 mM lithium sulfate, 300 mM sodium sulfate, 300 mM potassium sulfate, 20% (v/v) PEG8000, 40% (v/v) 1,5-pentanediol
Resolution 2.70 Å R-free 0.229
7QPD Structure of the human MHC I peptide-loading complex editing module Deposited 2022-01-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 25–505（481 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å

7 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PDIA3_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–248； UniProt 134–376 Author chain B； PDBConstruct 6–248； UniProt 134–376 Author chain C； PDBConstruct 6–248； UniProt 134–376

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9wqu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9wqu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9wqu
Deposition date deposition_date2025-09-11
最后修订 last_revision2025-10-01
Structure title titleb-b' domain fragment of ER-60 (ERp57) under microgravity
Keywords keywordsthioredoxin fold, endoplasmic reticulum, oxidative protein folding, ISOMERASE; ISOMERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.94 Å
Radius of gyration Rg (electron density) rg_electron35.03 Å
Forward intensity I(0) i0102248000.00
Molecular weight molecular_weight80506.0 kDa
Excluded volume excluded_volume100610 ų
Envelope volume envelope_volume134950 ų
Hydration-shell volume shell_volume35056 ų
Envelope diameter envelope_diameter131.6 Å
Shell Rg shell_rg37.65 Å
Envelope Rg envelope_rg35.05 Å
Shape Rg shape_rg35.04 Å
Total Rg total_rg35.21 Å
Total atoms total_atoms5683
Residues n_residues699
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax124.8 Å
Rg (real space) rg_real35.35 Å
Rg uncertainty (real space) rg_real_error1.62 Å
I(0) (real space) i0_real1.0220e+08
I(0) uncertainty (real space) i0_real_error1.9570e+06
Rg (reciprocal space) rg_reciprocal35.09 Å
I(0) (reciprocal space) i0_reciprocal102200000.0000
Solution quality estimate total_estimate0.7897
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.0 Å
Skewness Skewness skewness0.668
Kurtosis Kurtosis kurtosis0.075
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15890000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.662; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.734; Smooth: 0.540
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)