SAXSdb — 4rey

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Golgi reassembly-stacking protein 1

Homo sapiens

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–210	Fragment：GRASP domain of GRAS65, UNP residues 1-210	Golgin subfamily A member 2 × 1 （Q08379） SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；291 K；30% PEG 4000, 0.1M Tris, 0.2M Lithium sulfate, , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.96 Å R-free 0.190

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 4REY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6G8T Crystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the Golgin GM130 Deposited 2018-04-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–118（118 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；24% PEG1500, 20% glycerol	Resolution 2.67 Å R-free 0.258
6G8W Crystal Structures of the Single PDZ Domains from GRASP65 and their Interaction with the Golgin GM130 Deposited 2018-04-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 108–204（97 aa） Chain B 108–204（97 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；1.4M Na/K phosphate pH 8.2	Resolution 2.12 Å R-free 0.235

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GORS1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–213； UniProt 2–210

Golgin subfamily A member 2

Homo sapiens

UniProt Q08379

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 980–1002	Fragment：GM130 C-TERMINAL DOMAIN, UNP residues 980-1002	Golgi reassembly-stacking protein 1 × 1 （Q9BQQ3） SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；291 K；30% PEG 4000, 0.1M Tris, 0.2M Lithium sulfate, , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.96 Å R-free 0.190

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 4REY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6IW8 Crystal structure of Importin-alpha and wild-type GM130 Deposited 2018-12-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 13–60（48 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.1M Sodium malonate, 12% w/v Polyethylene glycol 3350 (pH 7.0)	Resolution 2.80 Å R-free 0.255
6IWA Crystal structure of Importin-alpha and phosphoserine GM130 Deposited 2018-12-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 25–52（28 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.1M Sodium citrate tribasic dihydrate, 16% w/v Polyethylene glycol 8000 (pH 5.5)	Resolution 2.40 Å R-free 0.216
6K06 Crystal structure of Importin-alpha and phosphomimetic GM130 Deposited 2019-05-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 13–60（48 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.2M Potassium thiocyante, 20% w/v Polyethylene glycol 3350	Resolution 1.75 Å R-free 0.199

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GOGA2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–27； UniProt 980–1002

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4rey
Deposition date deposition_date	2014-09-24
Structure title title	Crystal Structure of the GRASP65-GM130 C-terminal peptide complex
Keywords keywords	PDZ fold six-stranded anti parallel-barrel capped by two-helices, protein interaction, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.48 Å
Radius of gyration Rg (electron density) rg_electron	18.60 Å
Forward intensity I(0) i0	10933200.00
Molecular weight molecular_weight	24190.0 kDa
Excluded volume excluded_volume	30133 Å³
Envelope volume envelope_volume	35799 Å³
Hydration-shell volume shell_volume	16683 Å³
Envelope diameter envelope_diameter	68.4 Å
Shell Rg shell_rg	24.08 Å
Envelope Rg envelope_rg	18.82 Å
Shape Rg shape_rg	18.58 Å
Total Rg total_rg	19.50 Å
Total atoms total_atoms	3355
Residues n_residues	218
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	67.1 Å
Rg (real space) rg_real	19.49 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	1.0930e+07
I(0) uncertainty (real space) i0_real_error	1.4540e+05
Rg (reciprocal space) rg_reciprocal	19.49 Å
I(0) (reciprocal space) i0_reciprocal	10930000.0000
Solution quality estimate total_estimate	0.8599
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.8 Å
Skewness Skewness skewness	0.404
Kurtosis Kurtosis kurtosis	-0.124
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2063000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.742; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.987

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Golgi reassembly-stacking protein 1
Molecular weight formula_weight	23266.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3692

GPEIGLGVSAEQPAGGAEGFHLHGVQENSPAQQAGLEPYFDFIITIGHSRLNKENDTLKALLKANVEKPVKLEVFNMKTMRVREVEVVPSNMWGGQGLLGASVRFCSFRRASEQVWHVLDVEPSSPAALAGLRPYTDYVVGSDQILQESEDFFTLIESHEGKPLKLMVYNSKSDSCREVTVTPNAAWGGEGSLGCGIGYGYLHRIPTQPPSYH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Golgin subfamily A member 2
Molecular weight formula_weight	3060.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPEFGSNPCIPFFYRADENDEVKITVI

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	201

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4reyA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	4reyA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

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8. Citations (1)

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Unit-cell length a length_a	129.725 Å
Unit-cell length b length_b	129.725 Å
Unit-cell length c length_c	37.104 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	1.960 Å
Low-resolution limit resolution_low	64.860 Å
R factor r_factor	0.1550
R_work r_work	0.1520
R_free r_free	0.1900

fit	/app/data/saxs_computation/re/4rey/4rey.fit
pddf	/app/data/pr_computation/re/4rey/4rey.pr.out
profile	/app/data/saxs_computation/re/4rey/4rey.dat

Crystal Structure of the GRASP65-GM130 C-terminal peptide complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Golgi reassembly-stacking protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Golgin subfamily A member 2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)