SAXSdb — 6hm8

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

Golgi resident protein GCP60

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 364–528	Not recorded	Genome polyprotein × 1 （A0A2K9Y515）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；10% w/v PEG 8000, 6% v/v 1,5-pentanediol, 14% v/v PEG 200, 10 mM spermine, 10 mM spermidine, 10 mM DL-ornithine, 10 mM 1,4-diaminobutane, 200 mM NaCl, 100 mM GlyGly/AMPD pH 8.5	Resolution 2.28 Å R-free 0.233

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 6HM8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2N72 Solution structure of the Q domain from ACBD3 Deposited 2015-09-02	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 241–308（68 aa） Fragment：UNP residues 241-308	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.28 mM [U-13C; U-15N] protein, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2N73 Solution structure of the ACBD3:PI4KB complex Deposited 2015-09-02	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 241–308（68 aa） Fragment：UNP residues 241-308	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.47 mM [U-13C; U-15N] protein_1, 0.47 mM [U-13C; U-15N] protein_2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5LZ1 Crystal structure of human ACBD3 GOLD domain Deposited 2016-09-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 364–528（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100mM Tris pH 8.8, 25% w/v PEG 3.350, 20% glycerol, 20mM 2-propanol/1,2 -propanediol/1,3-propanediol/1-butanol/1,4-butanediol/1,6-hexanediol	Resolution 2.00 Å R-free 0.247
5LZ3 Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of Aichivirus A Deposited 2016-09-29	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 364–528（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100mM MOPS/HEPES pH 7.5, 12.5% w/v PEG 1.000, 12.5% w/v PEG 3.350, 12.5% v/v MPD, 20mM D-glucose/D-mannose/D-galactose/L-fucose/D-xylose/N-acetyl-D-glucosamine	Resolution 3.00 Å R-free 0.248
5LZ6 Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of Aichivirus B Deposited 2016-09-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 364–528（165 aa）	Not recorded	BGC beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100mM MOPSO/Bis-Tris pH 6.5, 15% w/v PEG 3.000, 1% w/v DDAO, 10% 1,4-butanediol, 10% w/v glucose, 20mM L-arginine/L-threonine/L-histidine/betaine, 10mM trans-4-hydroxy-L-proline	Resolution 2.60 Å R-free 0.260
5TDQ Crystal Structure of the GOLD domain of ACBD3 Deposited 2016-09-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 367–528（162 aa） Fragment：GOLD domain, UNP residues 367-528	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；13% PEG 4000, 200 mM Ammonium Sulfate, 100 mM HEPES, 10% 2-propanol, 10% glycerol	Resolution 2.49 Å R-free 0.262
6HLN Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of enterovirus-D68 Deposited 2018-09-11	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 364–528（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% w/v PEG 8000, 6% v/v 1,5-pentanediol, 14% v/v PEG 200, 10 mM spermine, 10 mM spermidine, 10 mM DL-ornithine, 10 mM 1,4-diaminobutane, 300 mM NaCl, 100 mM GlyGly/AMPD pH 8.5	Resolution 2.10 Å R-free 0.251
6HLT Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of rhinovirus-14 (HRV14) Deposited 2018-09-11	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 364–528（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% w/v PEG 8000, 20% v/v ethylene glycol, 30 mM MgCl2, 30 mM CaCl2, 100 mM bicine/Tris pH 8.5	Resolution 2.81 Å R-free 0.239
6HLT Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of rhinovirus-14 (HRV14) Deposited 2018-09-11	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 364–528（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% w/v PEG 8000, 20% v/v ethylene glycol, 30 mM MgCl2, 30 mM CaCl2, 100 mM bicine/Tris pH 8.5	Resolution 2.81 Å R-free 0.239
6HLV Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of poliovirus-1 (L24A mutant) Deposited 2018-09-11	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 364–528（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；12,5% w/v PEG 4000, 20% v/v 1,2,6-hexanetriol, 4% v/v tert-butanol, 1 mM rubidium chloride, 1 mM strontium chloride, 1 mM cesium acetate, 1 mM barium acetate, 100 mM GlyGly/AMPD pH 8.5	Resolution 2.50 Å R-free 0.241
6HLW Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of enterovirus-A71 (fusion protein) Deposited 2018-09-11	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 364–528（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；5% w/v PEG 20.000, 25% v/v 1,1,1-tris(hydroxymethyl)propane, 1% w/v NDSB 201, 0.5 mM MgCl2, 0.5mM CoCl2, 0.5 mM NiCl2, 0.5 mM ZnCl2, 100 mM BES/TEA pH 7.5	Resolution 2.73 Å R-free 0.256
6HLW Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of enterovirus-A71 (fusion protein) Deposited 2018-09-11	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 364–528（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；5% w/v PEG 20.000, 25% v/v 1,1,1-tris(hydroxymethyl)propane, 1% w/v NDSB 201, 0.5 mM MgCl2, 0.5mM CoCl2, 0.5 mM NiCl2, 0.5 mM ZnCl2, 100 mM BES/TEA pH 7.5	Resolution 2.73 Å R-free 0.256
6HMV Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of enterovirus-D68 (fusion protein, LVVY mutant) Deposited 2018-09-13	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 364–528（165 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 30 mM MgCl2, 30 mM CaCl2, 100 mM bicine/Tris pH 8.5	Resolution 2.24 Å R-free 0.265

11 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GCP60_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–168； UniProt 364–528

Genome polyprotein

Enterovirus D68

UniProt A0A2K9Y515

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 1454–1498	Not recorded	Golgi resident protein GCP60 × 1 （Q9H3P7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；10% w/v PEG 8000, 6% v/v 1,5-pentanediol, 14% v/v PEG 200, 10 mM spermine, 10 mM spermidine, 10 mM DL-ornithine, 10 mM 1,4-diaminobutane, 200 mM NaCl, 100 mM GlyGly/AMPD pH 8.5	Resolution 2.28 Å R-free 0.233

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 6HM8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6HMV Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of enterovirus-D68 (fusion protein, LVVY mutant) Deposited 2018-09-13	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1454–1498（45 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 30 mM MgCl2, 30 mM CaCl2, 100 mM bicine/Tris pH 8.5	Resolution 2.24 Å R-free 0.265

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A2K9Y515_9ENTO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–50； UniProt 1454–1498

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	6hm8
Deposition date deposition_date	2018-09-12
Structure title title	Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of enterovirus-D68 (fusion protein)
Keywords keywords	complex, Golgi, enterovirus, picornavirus, VIRAL PROTEIN; VIRAL 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	16.81 Å
Radius of gyration Rg (electron density) rg_electron	15.65 Å
Forward intensity I(0) i0	7172700.00
Molecular weight molecular_weight	19755.0 kDa
Excluded volume excluded_volume	24792 Å³
Envelope volume envelope_volume	27855 Å³
Hydration-shell volume shell_volume	14949 Å³
Envelope diameter envelope_diameter	57.4 Å
Shell Rg shell_rg	21.80 Å
Envelope Rg envelope_rg	16.11 Å
Shape Rg shape_rg	15.62 Å
Total Rg total_rg	16.84 Å
Total atoms total_atoms	1401
Residues n_residues	171
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	56.3 Å
Rg (real space) rg_real	16.72 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	7.1730e+06
I(0) uncertainty (real space) i0_real_error	9.2680e+04
Rg (reciprocal space) rg_reciprocal	16.73 Å
I(0) (reciprocal space) i0_reciprocal	7173000.0000
Solution quality estimate total_estimate	0.7939
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.204
Kurtosis Kurtosis kurtosis	-0.259
Angular range angular_range	— – 0.4750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2016000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.772; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Golgi resident protein GCP60
Molecular weight formula_weight	19389.3 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	1401

GAMESLPVIAAPSMWTRPQIKDFKEKIQQDADSVITVGRGEVVTVRVPTHEEGSYLFWEFATDNYDIGFGVYFEWTDSPNTAVSVHVSESSDDDEEEEENIGCEEKAKKNANKPLLDEIVPVYRRDCHEEVYAGSHQYPGRGVYLLKFDNSYSLWRSKSVYYRVYYTR

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Genome polyprotein
Molecular weight formula_weight	5511.1 kDa
EC 编号 ec_number	3.4.22.29,3.6.1.15,3.4.22.28,2.7.7.48
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSGSGTPAPDAINDLLRSVDSQEVRDYCQKKGWIVIHPSNELVVEKHISR

来源 Source

来源生物 organism	Enterovirus D68
NCBI Class编号 ncbi_taxonomy_id	42789
宿主生物 host_organism	Escherichia coli BL21(DE3)

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8. Citations (1)

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Unit-cell length a length_a	96.361 Å
Unit-cell length b length_b	55.659 Å
Unit-cell length c length_c	64.372 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.89 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.277 Å
Low-resolution limit resolution_low	41.220 Å
R factor r_factor	0.2186
R_work r_work	0.2177
R_free r_free	0.2332

fit	/app/data/saxs_computation/hm/6hm8/6hm8.fit
pddf	/app/data/pr_computation/hm/6hm8/6hm8.pr.out
profile	/app/data/saxs_computation/hm/6hm8/6hm8.dat

Crystal structure of human ACBD3 GOLD domain in complex with 3A protein of enterovirus-D68 (fusion protein)

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

Golgi resident protein GCP60

State in the Current Structure

Other States of the Same Protein in the Database

Genome polyprotein

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)