SAXSdb — 2veq

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

CENTROMERE DNA-BINDING PROTEIN COMPLEX CBF3 SUBUNIT B

SACCHAROMYCES CEREVISIAE

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 48–608	Fragment：RESIDUES 48-608	BME BETA-MERCAPTOETHANOL × 2 CAC CACODYLATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；100MM SODIUM CACODYLATE PH 6.5, 0.2M POTASSIUM THIOCYANATE, 12% PEG 4000	Resolution 2.49 Å R-free 0.246

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 2VEQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2QUQ Crystal Structure of the Essential Inner Kinetochore Protein Cep3p Deposited 2007-08-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 47–608（562 aa） Fragment：residues 47-608	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100 mM HEPES, 5% PEG 4000, 500 mM NaCl, pH 7.5, vapor diffusion, hanging drop, temperature 298K	Resolution 2.80 Å R-free 0.285
6F07 CBF3 Core Complex Deposited 2017-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–608（608 aa） Chain B 1–608（608 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6FE8 Cryo-EM structure of the core Centromere Binding Factor 3 complex Deposited 2017-12-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 47–608（562 aa） Chain B 47–608（562 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6GSA Core Centromere Binding Factor 3 (CBF3) with monomeric Ndc10 Deposited 2018-06-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: tetrameric	Chain A 47–608（562 aa） Chain B 47–608（562 aa）	Mutation：Truncation of the N-terminal domain, UNP residues 1-46 Mutation：Truncation of the N-terminal domain, UNP residues 1-46	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6GYP Cryo-EM structure of the CBF3-core-Ndc10-DBD complex of the budding yeast kinetochore Deposited 2018-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–608（608 aa） Chain C 49–608（560 aa）	Not recorded	MET METHIONINE × 1 PHE PHENYLALANINE × 1 ASN ASPARAGINE × 1 ARG ARGININE × 1 THR THREONINE × 2 GLN GLUTAMINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6GYS Cryo-EM structure of the CBF3-CEN3 complex of the budding yeast kinetochore Deposited 2018-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain B 1–608（608 aa） Chain C 1–608（608 aa） Chain I 1–608（608 aa） Chain J 1–608（608 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
6GYU Cryo-EM structure of the CBF3-msk complex of the budding yeast kinetochore Deposited 2018-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–608（608 aa） Chain C 49–608（560 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7K79 CBF3 Deposited 2020-09-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 1–608（608 aa） Chain O 1–608（608 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7K7G nucleosome and Gal4 complex Deposited 2020-09-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain M 1–48（48 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8OW1 Cryo-EM structure of the yeast Inner kinetochore bound to a CENP-A nucleosome. Deposited 2023-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric	Chain CE 1–608（608 aa） Chain ce 1–608（608 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CBF3B_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–565； UniProt 48–608

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	2veq
Deposition date deposition_date	2007-10-26
Structure title title	Insights into kinetochore-DNA interactions from the structure of Cep3p
Keywords keywords	;TRANSCRIPTION FACTOR, CELL CYCLE, ZINC, CEP3P, NUCLEUS, CENTROMERE, DNA-BINDING, PHOSPHORYLATION, CHROMOSOMAL PROTEIN, KINETOCHORE, CBF3 COMPLEX, METAL-BINDING ;; CELL CYCLE
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	25.70 Å
Radius of gyration Rg (electron density) rg_electron	24.58 Å
Forward intensity I(0) i0	56553400.00
Molecular weight molecular_weight	61377.0 kDa
Excluded volume excluded_volume	77926 Å³
Envelope volume envelope_volume	93521 Å³
Hydration-shell volume shell_volume	31163 Å³
Envelope diameter envelope_diameter	87.6 Å
Shell Rg shell_rg	32.35 Å
Envelope Rg envelope_rg	24.99 Å
Shape Rg shape_rg	24.58 Å
Total Rg total_rg	25.46 Å
Total atoms total_atoms	4327
Residues n_residues	520
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	83.5 Å
Rg (real space) rg_real	25.63 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	5.6550e+07
I(0) uncertainty (real space) i0_real_error	8.1030e+05
Rg (reciprocal space) rg_reciprocal	25.65 Å
I(0) (reciprocal space) i0_reciprocal	56550000.0000
Solution quality estimate total_estimate	0.8778
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.0 Å
Skewness Skewness skewness	0.305
Kurtosis Kurtosis kurtosis	-0.270
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12510000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.836

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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	CENTROMERE DNA-BINDING PROTEIN COMPLEX CBF3 SUBUNIT B
Molecular weight formula_weight	66378.8 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	4405

GSHMLITASSSKEYLPDLLLFWQNYEYWITNIGLYKTKQRDLTRTPANLDTDTEECMFWMNYLQKDQSFQLMNFAMENLGALYFGSIGDISELYLRVEQYWDRRADKNHSVDGKYWDALIWSVFTMCIYYMPVEKLAEIFSVYPLHEYLGSNKRLNWEDGMQLVMCQNFARCSLFQLKQCDFMAHPDIRLVQAYLILATTTFPYDEPLLANSLLTQCIHTFKNFHVDDFRPLLNDDPVESIAKVTLGRIFYRLCGCDYLQSGPRKPIALHTEVSSLLQHAAYLQDLPNVDVYREENSTEVLYWKIISLDRDLDQYLNKSSKPPLKTLDAIRRELDIFQYKVDSLEEDFRSNNSRFQKFIALFQISTVSWKLFKMYLIYYDTADSLLKVIHYSKVIISLIVNNFHAKSEFFNRHPMVMQTITRVVSFISFYQIFVESAAVKQLLVDLTELTANLPTIFGSKLDKLVYLTERLSKLKLLWDKVQLLDSGDSFYHPVFKILQNDIKIIELKNDEMFSLIKGLGSLVPLNKLRQESLLEEEDENNTEPSDFRTIVEEFQSEYNISDILS

来源 Source

来源生物 organism	SACCHAROMYCES CEREVISIAE
通用名 common_name	;BAKER'S YEAST ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 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	78

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8. Citations (1)

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Unit-cell length a length_a	83.737 Å
Unit-cell length b length_b	83.737 Å
Unit-cell length c length_c	231.368 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.490 Å
Low-resolution limit resolution_low	41.200 Å
R factor r_factor	0.2200
R_work r_work	0.2200
R_free r_free	0.2460

fit	/app/data/saxs_computation/ve/2veq/2veq.fit
pddf	/app/data/pr_computation/ve/2veq/2veq.pr.out
profile	/app/data/saxs_computation/ve/2veq/2veq.dat

Insights into kinetochore-DNA interactions from the structure of Cep3p

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

CENTROMERE DNA-BINDING PROTEIN COMPLEX CBF3 SUBUNIT 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