SAXSdb — 2cp8

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

Next to BRCA1 gene 1 protein

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 916–956	Fragment：UBA	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure ambient NMR sample composition：2.62mM RSGI RUH-046 U-13C, 15N; 20mM Tris-HCl U-2H, 100mM NaCl, 1mM DTT U-2H, 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 2CP8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WJ6 Solution structure of RSGI RUH-024, a PB1 domain in human cDNA, KIAA0049 Deposited 2004-05-29	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–88（88 aa） Fragment：PB1 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure ambient NMR sample composition 1.15mM PB1 domain U-15N,13C; 20mM Tris-HCl buffer (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2BKF Structure of the PB1 domain of NBR1 Deposited 2005-02-16	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–85（85 aa） Fragment：RESIDUES 1-85 (PB1 INTERACTION DOMAIN)	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.1；1.6 M AMMONIUM SULFATE,0.1 M SODIUM ACETATE PH 4.1	Resolution 1.56 Å R-free 0.226
2G4S Anomalous substructure of NBR1PB1 Deposited 2006-02-22	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–85（85 aa） Fragment：PB1 domain	Not recorded	CL CHLORIDE ION × 1 ACY ACETIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.15 Å R-free 0.323
2L8J GABARAPL-1 NBR1-LIR complex structure Deposited 2011-01-17	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 726–738（13 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.6 mM [U-98% 15N] GABARAPL-1, 0.9 mM NBR1-LIR, 50 mM sodium phosphate, 100 mM sodium chloride, 4.6 mM sodium azide, 1 mM protease inhibitor cocktail, 0.3 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.6 mM [U-98% 13C; U-98% 15N] GABARAPL-1, 0.9 mM NBR1-LIR, 50 mM sodium phosphate, 100 mM sodium chloride, 4.6 mM sodium azide, 1 mM protease inhibitor cocktail, 0.3 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.9 mM GABARAPL-1, 0.6 mM [U-98% 15N] NBR1-LIR, 50 mM sodium phosphate, 100 mM sodium chloride, 4.6 mM sodium azide, 1 mM protease inhibitor cocktail, 0.3 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.9 mM GABARAPL-1, 0.6 mM [U-98% 13C; U-98% 15N] NBR1-LIR, 50 mM sodium phosphate, 100 mM sodium chloride, 4.6 mM sodium azide, 1 mM protease inhibitor cocktail, 0.3 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2MGW Solution Structure of the UBA Domain of Human NBR1 Deposited 2013-11-09	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 913–959（47 aa） Fragment：UNP residues 913-959	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.6；298 K；Pressure ambient NMR sample composition 20 mM potassium phosphate-1, 5 mM potassium chloride-2, 1 mM EDTA-3, 1 mM benzamidine-4, 1 mM DTT-5, 0.02 % sodium azide-6, 1.2 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-7, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 20 mM potassium phosphate-8, 5 mM potassium chloride-9, 1 mM EDTA-10, 1 mM benzamidine-11, 1 mM DTT-12, 0.02 % sodium azide-13, 0.5 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-14, 12.5 mg/mL Pf1 phage-15, 150 mM sodium chloride-16, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2MJ5 Structure of the UBA Domain of Human NBR1 in Complex with Ubiquitin Deposited 2013-12-25	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 913–959（47 aa） Fragment：UNP residues 916-959	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.6；298 K；Pressure ambient NMR sample composition 20 mM potassium phosphate-1, 5 mM potassium chloride-2, 1 mM EDTA-3, 1 mM benzamidine-4, 1 mM DTT-5, 0.02 % sodium azide-6, 1.2 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-7, 95 % H2O-8, 5 % D2O-9, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 20 mM potassium phosphate-10, 5 mM potassium chloride-11, 1 mM EDTA-12, 1 mM benzamidine-13, 1 mM DTT-14, 0.02 % sodium azide-15, 0.5 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-16, 12.5 mg/mL Pf1 phage-17, 150 mM sodium chloride-18, 95 % H2O-19, 5 % D2O-20, 0.5 mM [U-100% 13C; U-100% 15N] NBR1_UBA-21, 2 mM Ubiquitin-22, 12.5 mg/mL Pf1 phage-23, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 20 mM potassium phosphate-24, 5 mM potassium chloride-25, 1 mM EDTA-26, 1 mM benzamidine-27, 1 mM DTT-28, 0.02 % sodium azide-29, 0.5 mM [U-100% 13C; U-100% 15N] NBR1 residues 913-959-30, 12.5 mg/mL Pf1 phage-31, 150 mM sodium chloride-32, 95 % H2O-33, 5 % D2O-34, 0.5 mM [U-100% 13C; U-100% 15N] NBR1_UBA-35, 2 mM Ubiquitin-36, 12.5 mg/mL Pf1 phage-37, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 2 mM NBR1_UBA-38, 0.5 mM [U-100% 13C; U-100% 15N] Ubiquitin-39, 12.5 mg/mL Pf1 phage-40, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1 mM [U-100% 15N] NBR1_UBA-41, 4.5 mM Ubiquitin-42, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
4OLE Crystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo sapiens at 2.52 A resolution Deposited 2014-01-23	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 365–485（121 aa） Fragment：UNP residues 365-485	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.33；277 K；2.35M ammonium sulfate, 0.1M TRIS pH 8.33, 0.01M Adenosine-5'-triphosphate disodium salt hydrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.52 Å R-free 0.188
4OLE Crystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo sapiens at 2.52 A resolution Deposited 2014-01-23	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 365–485（121 aa） Fragment：UNP residues 365-485	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.33；277 K；2.35M ammonium sulfate, 0.1M TRIS pH 8.33, 0.01M Adenosine-5'-triphosphate disodium salt hydrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.52 Å R-free 0.188
4OLE Crystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo sapiens at 2.52 A resolution Deposited 2014-01-23	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 365–485（121 aa） Fragment：UNP residues 365-485	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.33；277 K；2.35M ammonium sulfate, 0.1M TRIS pH 8.33, 0.01M Adenosine-5'-triphosphate disodium salt hydrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.52 Å R-free 0.188
4OLE Crystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo sapiens at 2.52 A resolution Deposited 2014-01-23	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 365–485（121 aa） Fragment：UNP residues 365-485	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.33；277 K；2.35M ammonium sulfate, 0.1M TRIS pH 8.33, 0.01M Adenosine-5'-triphosphate disodium salt hydrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.52 Å R-free 0.188
4OLE Crystal structure of a neighbor of BRCA1 gene 1 (NBR1) from Homo sapiens at 2.52 A resolution Deposited 2014-01-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 16 PDB declaration: hexadecameric	Chain A 365–485（121 aa） Fragment：UNP residues 365-485 Chain B 365–485（121 aa） Fragment：UNP residues 365-485 Chain C 365–485（121 aa） Fragment：UNP residues 365-485 Chain D 365–485（121 aa） Fragment：UNP residues 365-485	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 28 EDO 1,2-ETHANEDIOL × 36	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.33；277 K；2.35M ammonium sulfate, 0.1M TRIS pH 8.33, 0.01M Adenosine-5'-triphosphate disodium salt hydrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.52 Å R-free 0.188

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

View Construct and Data Evidence

UniProt name	NBR1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–48； UniProt 916–956

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	2cp8
Deposition date deposition_date	2005-05-19
Structure title title	Solution structure of the RSGI RUH-046, a UBA domain from human Next to BRCA1 gene 1 protein (KIAA0049 protein) R923H variant
Keywords keywords	;UBA domain, structural genomics, human, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, PROTEIN BINDING ;; PROTEIN BINDING
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	12.32 Å
Radius of gyration Rg (electron density) rg_electron	11.57 Å
Forward intensity I(0) i0	200289000.00
Molecular weight molecular_weight	116070.0 kDa
Excluded volume excluded_volume	144500 Å³
Envelope volume envelope_volume	24289 Å³
Hydration-shell volume shell_volume	12764 Å³
Envelope diameter envelope_diameter	61.7 Å
Shell Rg shell_rg	22.34 Å
Envelope Rg envelope_rg	17.95 Å
Shape Rg shape_rg	11.55 Å
Total Rg total_rg	11.99 Å
Total atoms total_atoms	16360
Residues n_residues	1080
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	32.0 Å
Rg (real space) rg_real	11.46 Å
Rg uncertainty (real space) rg_real_error	0.04 Å
I(0) (real space) i0_real	1.9040e+08
I(0) uncertainty (real space) i0_real_error	1.5210e+06
Rg (reciprocal space) rg_reciprocal	12.51 Å
I(0) (reciprocal space) i0_reciprocal	200300000.0000
Solution quality estimate total_estimate	0.6744
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	14.6 Å
Skewness Skewness skewness	0.242
Kurtosis Kurtosis kurtosis	-0.279
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	4.3430
Highest regularization parameter α highest_alpha	42260.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.005; Oscil: 0.937; Stabil: 0.986; Sysdev: 0.000; 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 (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2cp8a1
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.1 — UBA domain

Domain ID domain_id	d2cp8a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2cp8a3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2cp8A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

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8. Citations (1)

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Description description	Next to BRCA1 gene 1 protein
Molecular weight formula_weight	5825.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	16360

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

fit	/app/data/saxs_computation/cp/2cp8/2cp8.fit
pddf	/app/data/pr_computation/cp/2cp8/2cp8.pr.out
profile	/app/data/saxs_computation/cp/2cp8/2cp8.dat

Solution structure of the RSGI RUH-046, a UBA domain from human Next to BRCA1 gene 1 protein (KIAA0049 protein) R923H variant

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

Next to BRCA1 gene 1 protein

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)