SAXSdb — 8jca

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

ADP-ribosylation factor-like protein 8B

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 18–186	Mutation：Q75L	Pleckstrin homology domain-containing family M member 2 × 1 （Q8IWE5） GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298 K；800mM Potassiam phosphate dibasic 1.2 M Sodium phosphate monobasic 0.1M CAPS/Sodium hydroxide 0.2M Lithium sulfate pH10.5	Resolution 1.65 Å R-free 0.206

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 8JCA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2AL7 Structure Of Human ADP-Ribosylation Factor-Like 10C Deposited 2005-08-04	Different construct Different mutation/modification 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 18–184（167 aa）	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；PEG 3350 25%, Ammonium Acetate 100mM, 100mM HEPES (7.5), VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.85 Å R-free 0.251
8JC5 Crystal structure of PLEKHM1 RUN domain in complex with GTP-bound Arl8b(Q75L) Deposited 2023-05-10	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 18–186（169 aa）	Mutation：Q75L	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Lithium chloride, 0.1 M TRIS pH=7.6, 18% (w/v) PEG 8000	Resolution 2.01 Å R-free 0.201
8JC5 Crystal structure of PLEKHM1 RUN domain in complex with GTP-bound Arl8b(Q75L) Deposited 2023-05-10	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 18–186（169 aa）	Mutation：Q75L	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.2 M Lithium chloride, 0.1 M TRIS pH=7.6, 18% (w/v) PEG 8000	Resolution 2.01 Å R-free 0.201

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

View Construct and Data Evidence

UniProt name	ARL8B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–169； UniProt 18–186

Pleckstrin homology domain-containing family M member 2

Homo sapiens

UniProt Q8IWE5

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 1–165	Not recorded	ADP-ribosylation factor-like protein 8B × 1 （Q9NVJ2） GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298 K；800mM Potassiam phosphate dibasic 1.2 M Sodium phosphate monobasic 0.1M CAPS/Sodium hydroxide 0.2M Lithium sulfate pH10.5	Resolution 1.65 Å R-free 0.206

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 8JCA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3CXB Crystal Structure of sifa and skip Deposited 2008-04-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 773–884（112 aa） Fragment：PH motif, UNP residues 773-884	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% Poly acrylic acid5100, 0.05M magnesium chloride, 0.1M Hepes, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.288
3HW2 Crystal structure of the SifA-SKIP(PH) complex Deposited 2009-06-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 771–875（105 aa） Fragment：Pleskrin homology (PH) domain, UNP residues 771-876	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；30% PEG 4000, 0.2M Na acetate trihydrate, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.30 Å R-free 0.309
3ZFW Crystal structure of the TPR domain of kinesin light chain 2 in complex with a tryptophan-acidic cargo peptide Deposited 2012-12-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 203–212（10 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.10 M MES PH 6.5, 0.2 L-PROLINE, 7% PGA	Resolution 2.90 Å R-free 0.244
3ZFW Crystal structure of the TPR domain of kinesin light chain 2 in complex with a tryptophan-acidic cargo peptide Deposited 2012-12-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 203–212（10 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.10 M MES PH 6.5, 0.2 L-PROLINE, 7% PGA	Resolution 2.90 Å R-free 0.244

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PKHM2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–165； UniProt 1–165

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	8jca
Deposition date deposition_date	2023-05-10
最后修订 last_revision	2024-03-27
Structure title title	Cyrstal structure of SKIP RUN domain in complex with GTP-bound Arl8b(Q75L)
Keywords keywords	SKIP, RUN, Arl8b, GTP-bound, GTPase, Arf, PROTEIN BINDING; PROTEIN BINDING
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	22.51 Å
Radius of gyration Rg (electron density) rg_electron	21.45 Å
Forward intensity I(0) i0	25090400.00
Molecular weight molecular_weight	38422.0 kDa
Excluded volume excluded_volume	48206 Å³
Envelope volume envelope_volume	56512 Å³
Hydration-shell volume shell_volume	22133 Å³
Envelope diameter envelope_diameter	77.3 Å
Shell Rg shell_rg	27.97 Å
Envelope Rg envelope_rg	21.75 Å
Shape Rg shape_rg	21.45 Å
Total Rg total_rg	22.31 Å
Total atoms total_atoms	2703
Residues n_residues	329
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	75.4 Å
Rg (real space) rg_real	22.48 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	2.5090e+07
I(0) uncertainty (real space) i0_real_error	3.1640e+05
Rg (reciprocal space) rg_reciprocal	22.49 Å
I(0) (reciprocal space) i0_reciprocal	25090000.0000
Solution quality estimate total_estimate	0.8832
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.1 Å
Skewness Skewness skewness	0.285
Kurtosis Kurtosis kurtosis	-0.476
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4879000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	ADP-ribosylation factor-like protein 8B
Molecular weight formula_weight	19400.4 kDa
EC 编号 ec_number	3.6.5.2
Mutation mutation	Q75L
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	2999

KEEMELTLVGLQYSGKTTFVNVIASGQFSEDMIPTVGFNMRKVTKGNVTIKIWDIGGLPRFRSMWERYCRGVNAIVYMIDAADREKIEASRNELHNLLDKPQLQGIPVLVLGNKRDLPNALDEKQLIEKMNLSAIQDREICCYSISCKEKDNIDITLQWLIQHSKSRRS

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	Pleckstrin homology domain-containing family M member 2
Molecular weight formula_weight	19180.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MEPGEVKDRILENISLSVKKLQSYFAACEDEIPAIRNHDKVLQRLCEHLDHALLYGLQDLSSGYWVLVVHFTRREAIKQIEVLQHVATNLGRSRAWLYLALNENSLESYLRLFQENLGLLHKYYVKNALVCSHDHLTLFLTLVSGLEFIRFELDLDAPYLDLAPY

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	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	296

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8. Citations (1)

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Unit-cell length a length_a	178.687 Å
Unit-cell length b length_b	53.836 Å
Unit-cell length c length_c	40.512 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.13 °
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	1.650 Å
Low-resolution limit resolution_low	32.050 Å
R factor r_factor	0.1761
R_work r_work	0.1746
R_free r_free	0.2060

fit	/app/data/saxs_computation/jc/8jca/8jca.fit
pddf	/app/data/pr_computation/jc/8jca/8jca.pr.out
profile	/app/data/saxs_computation/jc/8jca/8jca.dat

Cyrstal structure of SKIP RUN domain in complex with GTP-bound Arl8b(Q75L)

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

ADP-ribosylation factor-like protein 8B

State in the Current Structure

Other States of the Same Protein in the Database

Pleckstrin homology domain-containing family M 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 (5)

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 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)