SAXSdb — 1gvd

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

MYB PROTO-ONCOGENE PROTEIN

OrganismNot specified

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 90–141	Fragment：R2, RESIDUES 90-141 Mutation：YES	NH4 AMMONIUM ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.8；297 K；3.15 M AMMONIUM SULFATE IN 0.05 M MES BUFFER AT PH 6.8, PROTEIN CONCENTRATION 10 MG/ML PLUS 10 MM DTT, TEMPERATURE 297 K	Resolution 1.45 Å R-free 0.195

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 1GVD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GUU CRYSTAL STRUCTURE OF C-MYB R1 Deposited 2002-01-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 38–89（52 aa） Fragment：R1, RESIDUES 38-89	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；1.6-1.7 M SODIUM CITRATE PH 6.8, PROTEIN CONCENTRATION 15 MG/ML, CRYSTAL WAS TRANSFORMED TO LOW HUMIDITY FORM AND FLASH COOLED, 1-2% V/V OF GLYCEROL WAS ADDED TO PREVENT THE CRYSTAL CRACKING DURING THE FLASH COOLING	Resolution 1.60 Å R-free 0.223
1GV2 CRYSTAL STRUCTURE OF C-MYB R2R3 Deposited 2002-02-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 89–193（105 aa） Fragment：R2R3, RESIDUES 89-193	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；1.6-1.7 M SODIUM CITRATE PH 6.8, PROTEIN CONCENTRATION 15 MG/ML, CRYSTAL WAS GROWN BY REPEATED MACROSEEDING, TRANSFORMED TO LOW HUMIDITY FORM AND FLASH COOLED, 1-2% V/V OF GLYCEROL WAS ADDED TO SODIUM CITRATE TO PREVENT THE CRYSTAL CRACKING DURING THE FLASH COOLING	Resolution 1.68 Å R-free 0.210
1GV5 CRYSTAL STRUCTURE OF C-MYB R2 Deposited 2002-02-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 90–141（52 aa） Fragment：R2, RESIDUES 90-141	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.8；297 K；1.65 M SODIUM CITRATE PH 6.8, PROTEIN CONCENTRATION 10 MG/ML PLUS 10 MM DTT, TEMPERATURE 297 K	Resolution 1.58 Å R-free 0.190
1H88 CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX1 Deposited 2001-01-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain C 35–193（159 aa） Fragment：RESIDUES 35-193	Mutation：YES	NH4 AMMONIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；297 K；0.05 M AMMONIUM ACETATE, 0.01 M MAGNESIUM CHLORIDE, 10% V/V MPD, 6% V/V GLYCEROL, 0.05 M TRIS HCL BUFFER PH 7.5 AT 24 DEGREES C	Resolution 2.80 Å R-free 0.277
1IDY STRUCTURE OF MYB TRANSFORMING PROTEIN, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-08-15	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 141–193（53 aa）	Mutation：P140M, I155L	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；283 K	Resolution not provided
1IDZ STRUCTURE OF MYB TRANSFORMING PROTEIN, NMR, 20 STRUCTURES Deposited 1996-08-15	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 141–193（53 aa）	Mutation：P140M, I155L	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；283 K	Resolution not provided
1MBE MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 1 Deposited 1995-05-19	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 38–89（52 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；290 K NMR measurement conditions pH 6.8；300 K	Resolution not provided
1MBF MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 1 Deposited 1995-05-19	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 38–89（52 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；290 K NMR measurement conditions pH 6.8；300 K	Resolution not provided
1MBG MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 2 Deposited 1995-05-19	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 90–141（52 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；290 K	Resolution not provided
1MBH MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 2 Deposited 1995-05-19	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 90–141（52 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；290 K	Resolution not provided
1MBJ MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 3 Deposited 1995-05-19	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 142–193（52 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；290 K NMR measurement conditions pH 6.8；300 K	Resolution not provided
1MBK MOUSE C-MYB DNA-BINDING DOMAIN REPEAT 3 Deposited 1995-05-19	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 142–193（52 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；290 K NMR measurement conditions pH 6.8；300 K	Resolution not provided
1MSE SOLUTION STRUCTURE OF A SPECIFIC DNA COMPLEX OF THE MYB DNA-BINDING DOMAIN WITH COOPERATIVE RECOGNITION HELICES Deposited 1995-01-24	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 Monomer；Protein × 1 PDB declaration: trimeric	Chain C 90–193（104 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；310 K	Resolution not provided
1MSF SOLUTION STRUCTURE OF A SPECIFIC DNA COMPLEX OF THE MYB DNA-BINDING DOMAIN WITH COOPERATIVE RECOGNITION HELICES Deposited 1995-01-24	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 Monomer；Protein × 1 PDB declaration: trimeric	Chain C 90–193（104 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1SB0 Solution structure of the KIX domain of CBP bound to the transactivation domain of c-Myb Deposited 2004-02-09	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 × 2 PDB declaration: dimeric	Chain B 291–315（25 aa） Fragment：transcriptional activation domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；27 K；Ionic strength (raw mmCIF value) 50 mM；Pressure ambient NMR sample composition 20 mM Tris d11 acetate d4; 50 mM NaCl; 2 mM NaN3; pH 5.5 \| 90% H20; 10% D2O	Resolution not provided
2AGH Structural basis for cooperative transcription factor binding to the CBP coactivator Deposited 2005-07-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 291–315（25 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；298 K；Pressure 1 NMR sample composition 0.5-0.8 mM 15N,13C-labeled protein (e.g. CBP) + 3 fold excess of unlabeled binding partners (MYB + MLL), 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O \| 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O NMR sample composition 13C,15N-MYB + UNLABELED CBP & MYB, 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O \| 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O NMR sample composition 13C,15N-MLL + UNLABELED CBP & MLL, 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O \| 20 mM Tris-d3-acetate, 50 mM NaCl, 0.2% sodium azide, 10% D2O	Resolution not provided
6DMX HBZ56 in complex with KIX and c-Myb Deposited 2018-06-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 284–315（32 aa） Fragment：residues 284-315 Chain C 284–315（32 aa） Fragment：residues 284-315	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, ammonium iodide	Resolution 2.80 Å R-free 0.301
6DMX HBZ56 in complex with KIX and c-Myb Deposited 2018-06-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 284–315（32 aa） Fragment：residues 284-315 Chain H 284–315（32 aa） Fragment：residues 284-315	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, ammonium iodide	Resolution 2.80 Å R-free 0.301
6DNQ HBZ77 in complex with KIX and c-Myb Deposited 2018-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 284–315（32 aa） Fragment：residues 284-315 Chain C 284–315（32 aa） Fragment：residues 284-315	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, calcium chloride	Resolution 2.35 Å R-free 0.229

18 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MYB_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–52； UniProt 90–141

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	1gvd
Deposition date deposition_date	2002-02-08
Structure title title	CRYSTAL STRUCTURE OF C-MYB R2 V103L MUTANT
Keywords keywords	TRANSCRIPTION, TRANSCRIPTION REGULATION, MYB, C-MYB, DNA BINDING, ION BINDING, PROTO-ONCOGENE, NUCLEAR PROTEIN; TRANSCRIPTION
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	11.97 Å
Radius of gyration Rg (electron density) rg_electron	10.51 Å
Forward intensity I(0) i0	1074990.00
Molecular weight molecular_weight	6518.0 kDa
Excluded volume excluded_volume	8110 Å³
Envelope volume envelope_volume	9157 Å³
Hydration-shell volume shell_volume	7632 Å³
Envelope diameter envelope_diameter	37.7 Å
Shell Rg shell_rg	15.85 Å
Envelope Rg envelope_rg	11.03 Å
Shape Rg shape_rg	10.43 Å
Total Rg total_rg	12.24 Å
Total atoms total_atoms	457
Residues n_residues	52
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	39.2 Å
Rg (real space) rg_real	11.90 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	1.0750e+06
I(0) uncertainty (real space) i0_real_error	1.1820e+04
Rg (reciprocal space) rg_reciprocal	11.90 Å
I(0) (reciprocal space) i0_reciprocal	1075000.0000
Solution quality estimate total_estimate	0.8707
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.4 Å
Skewness Skewness skewness	0.160
Kurtosis Kurtosis kurtosis	-0.185
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	229400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.788; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.954

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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	MYB PROTO-ONCOGENE PROTEIN
Molecular weight formula_weight	6316.4 kDa
Mutation mutation	YES
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	553

LIKGPWTKEEDQRLIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLNPE

Entity 2 Entity 2 non-polymer

Description description	AMMONIUM ION
Molecular weight formula_weight	18.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	51

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1gvda_
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.4.1.3 — Myb/SANT domain

CATH v4.4 (1 domains)

Domain ID domain_id	1gvdA00
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 (3)

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Unit-cell length a length_a	28.951 Å
Unit-cell length b length_b	40.114 Å
Unit-cell length c length_c	48.807 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	12.450 Å
R factor r_factor	0.1800
R_work r_work	0.1800
R_free r_free	0.1950

fit	/app/data/saxs_computation/gv/1gvd/1gvd.fit
pddf	/app/data/pr_computation/gv/1gvd/1gvd.pr.out
profile	/app/data/saxs_computation/gv/1gvd/1gvd.dat

CRYSTAL STRUCTURE OF C-MYB R2 V103L MUTANT

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

MYB PROTO-ONCOGENE 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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction