SAXSdb — 1hlv

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

MAJOR CENTROMERE AUTOANTIGEN B

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–DNA Monomer Protein × 1 DNA 2 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 1–129	Fragment：DNA BINDING DOMAIN	CENP-B BOX DNA × 1 CENP-B BOX DNA × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；MPD, potassium cacodylate, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.260

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 1HLV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BW6 HUMAN CENTROMERE PROTEIN B (CENP-B) DNA BINDIGN DOMAIN RP1 Deposited 1998-09-30	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 1–56（56 aa） Fragment：DNA-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 400 mM NA2SO4	Resolution not provided
1UFI Crystal structure of the dimerization domain of human CENP-B Deposited 2003-05-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 540–599（60 aa） Fragment：dimerization domain Chain B 540–599（60 aa） Fragment：dimerization domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.7；293 K；sodium citrate, CHES, pH 9.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.309
1UFI Crystal structure of the dimerization domain of human CENP-B Deposited 2003-05-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 540–599（60 aa） Fragment：dimerization domain Chain D 540–599（60 aa） Fragment：dimerization domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.7；293 K；sodium citrate, CHES, pH 9.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.309
1UFI Crystal structure of the dimerization domain of human CENP-B Deposited 2003-05-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 540–599（60 aa） Fragment：dimerization domain Chain B 540–599（60 aa） Fragment：dimerization domain Chain C 540–599（60 aa） Fragment：dimerization domain Chain D 540–599（60 aa） Fragment：dimerization domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.7；293 K；sodium citrate, CHES, pH 9.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.309
6KDR Crystal structure of human NRMT2 in complex with human centromere protein B peptide Deposited 2019-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 2–10（9 aa） Chain E 2–10（9 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 GOL GLYCEROL × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.3；291 K；0.1M Tris pH 8.3, 6% w/v Polyethylene glycol 8000	Resolution 2.11 Å R-free 0.205

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CENPB_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–129； UniProt 1–129

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	1hlv
Deposition date deposition_date	2000-12-04
Structure title title	CRYSTAL STRUCTURE OF CENP-B(1-129) COMPLEXED WITH THE CENP-B BOX DNA
Keywords keywords	;HELIX-TURN-HELIX, PROTEIN-DNA COMPLEX, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, DNA BINDING PROTEIN-DNA COMPLEX ;; DNA BINDING PROTEIN/DNA
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	21.51 Å
Radius of gyration Rg (electron density) rg_electron	20.98 Å
Forward intensity I(0) i0	22559900.00
Molecular weight molecular_weight	28046.0 kDa
Excluded volume excluded_volume	31588 Å³
Envelope volume envelope_volume	40838 Å³
Hydration-shell volume shell_volume	17210 Å³
Envelope diameter envelope_diameter	72.2 Å
Shell Rg shell_rg	26.30 Å
Envelope Rg envelope_rg	21.15 Å
Shape Rg shape_rg	20.93 Å
Total Rg total_rg	21.67 Å
Total atoms total_atoms	1921
Residues n_residues	173
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	69.4 Å
Rg (real space) rg_real	21.62 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	2.2560e+07
I(0) uncertainty (real space) i0_real_error	2.6290e+05
Rg (reciprocal space) rg_reciprocal	21.60 Å
I(0) (reciprocal space) i0_reciprocal	22560000.0000
Solution quality estimate total_estimate	0.8881
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.4 Å
Skewness Skewness skewness	0.421
Kurtosis Kurtosis kurtosis	-0.441
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2326000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.901; Smooth: 0.946

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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	CENP-B BOX DNA
Molecular weight formula_weight	6494.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	2019

GCCTTCGTTGGAAACGGGATT

Entity 2 Entity 2 polymer

Description description	CENP-B BOX DNA
Molecular weight formula_weight	6392.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

AATCCCGTTTCCAACGAAGGC

Entity 3 Entity 3 polymer

Description description	MAJOR CENTROMERE AUTOANTIGEN B
Molecular weight formula_weight	15169.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MGPKRRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKRAILASERKYGVASTCRKTNKLSPYDKLEGLLIAWFQQIRAAGLPVKGIILKEKALRIAEELGMDDFTASNGWLDRFRRRRS

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 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	98

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1hlva1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.7 — Centromere-binding

Domain ID domain_id	d1hlva2
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.1 — Homeodomain-like
Family Family family	a.4.1.7 — Centromere-binding

Domain ID domain_id	d1hlva3
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 (2 domains)

Domain ID domain_id	1hlvA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	1hlvA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

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8. Citations (1)

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Unit-cell length a length_a	83.374 Å
Unit-cell length b length_b	83.374 Å
Unit-cell length c length_c	139.021 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 31 1 2
Space-group number int_tables_number	151
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2219
R_work r_work	0.2219
R_free r_free	0.2599

fit	/app/data/saxs_computation/hl/1hlv/1hlv.fit
pddf	/app/data/pr_computation/hl/1hlv/1hlv.pr.out
profile	/app/data/saxs_computation/hl/1hlv/1hlv.dat

CRYSTAL STRUCTURE OF CENP-B(1-129) COMPLEXED WITH THE CENP-B BOX DNA

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

MAJOR CENTROMERE AUTOANTIGEN B

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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)