SAXSdb — 1gv2

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

MYB PROTO-ONCOGENE PROTEIN

Mus Musculus

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 89–193	Fragment：R2R3, RESIDUES 89-193	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

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 1GV2	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 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
1GV5 CRYSTAL STRUCTURE OF C-MYB R2 Deposited 2002-02-06	Different construct 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
1GVD CRYSTAL STRUCTURE OF C-MYB R2 V103L MUTANT Deposited 2002-02-08	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 90–141（52 aa） 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
1H88 CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX1 Deposited 2001-01-29	Different construct Different mutation/modification 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 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 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 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 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 1–105； UniProt 89–193

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	1gv2
Deposition date deposition_date	2002-02-05
Structure title title	CRYSTAL STRUCTURE OF C-MYB R2R3
Keywords keywords	TRANSCRIPTION, MYB, C-MYB, DNA BINDING, ION BINDING; 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	16.09 Å
Radius of gyration Rg (electron density) rg_electron	15.36 Å
Forward intensity I(0) i0	3081700.00
Molecular weight molecular_weight	12316.0 kDa
Excluded volume excluded_volume	15446 Å³
Envelope volume envelope_volume	18639 Å³
Hydration-shell volume shell_volume	10877 Å³
Envelope diameter envelope_diameter	51.5 Å
Shell Rg shell_rg	19.89 Å
Envelope Rg envelope_rg	15.52 Å
Shape Rg shape_rg	15.31 Å
Total Rg total_rg	16.42 Å
Total atoms total_atoms	869
Residues n_residues	103
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	52.2 Å
Rg (real space) rg_real	16.12 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	3.0820e+06
I(0) uncertainty (real space) i0_real_error	3.4980e+04
Rg (reciprocal space) rg_reciprocal	16.12 Å
I(0) (reciprocal space) i0_reciprocal	3082000.0000
Solution quality estimate total_estimate	0.8772
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.8 Å
Skewness Skewness skewness	0.349
Kurtosis Kurtosis kurtosis	-0.470
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1169000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.952; Smooth: 0.974

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	MYB PROTO-ONCOGENE PROTEIN
Molecular weight formula_weight	12674.7 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	941

ELIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLNPEVKKTSWTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV

来源 Source

来源生物 organism	Mus Musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	60

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1gv2a1
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

Domain ID domain_id	d1gv2a2
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 (2 domains)

Domain ID domain_id	1gv2A01
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	1gv2A02
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 (2)

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Unit-cell length a length_a	38.722 Å
Unit-cell length b length_b	28.250 Å
Unit-cell length c length_c	44.129 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.87 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.680 Å
Low-resolution limit resolution_low	44.120 Å
R factor r_factor	0.1930
R_work r_work	0.1930
R_free r_free	0.2100

fit	/app/data/saxs_computation/gv/1gv2/1gv2.fit
pddf	/app/data/pr_computation/gv/1gv2/1gv2.pr.out
profile	/app/data/saxs_computation/gv/1gv2/1gv2.dat

CRYSTAL STRUCTURE OF C-MYB R2R3

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