SAXSdb — 1h88

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

CCAAT/ENHANCER BINDING PROTEIN BETA

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 Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain A； UniProt 259–336 Chain B； UniProt 259–336	Fragment：RESIDUES 259-336	MYB PROTO-ONCOGENE PROTEIN × 1 （P06876） ;DNA(5'-(GPAPTPGPTPGPGPCPGPCPAP APTPCPCPTPTPAPAPCPGPGPAPCPTPG)-3') ; × 1 ;DNA(5'-(CPCPAPGPTPCPCPGPTPTPAP APGPGPAPTPTPGPCPGPCPCPAPCPAPT)-3') ; × 1 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

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 1H88	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GTW crystal structure of C/EBPbeta bZip homodimer bound to a DNA fragment from the tom-1A promoter Deposited 2002-01-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: octameric	Chain A 259–336（78 aa） Fragment：BZIP DOMAIN, RESIDUES 259-336 Chain B 259–336（78 aa） Fragment：BZIP DOMAIN, RESIDUES 259-336	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.2 M POTASSIUM CHLORIDE, 0.1 M MAGNESIUM ACETATE, 10.0% W/V PEG 8000, 0.05 M SODIUM CACODYLATE CACODYLATE BUFFER PH 6.5, PROTEIN-DNA COMPLEX SOLUTION CONTAINS 0.01 M DTT AND 0.005 M NAN3, PROTEIN:DNA RATIO IS 1:1.2	Resolution 1.85 Å R-free 0.271
1GTW crystal structure of C/EBPbeta bZip homodimer bound to a DNA fragment from the tom-1A promoter Deposited 2002-01-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 259–336（78 aa） Fragment：BZIP DOMAIN, RESIDUES 259-336 Chain B 259–336（78 aa） Fragment：BZIP DOMAIN, RESIDUES 259-336	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.2 M POTASSIUM CHLORIDE, 0.1 M MAGNESIUM ACETATE, 10.0% W/V PEG 8000, 0.05 M SODIUM CACODYLATE CACODYLATE BUFFER PH 6.5, PROTEIN-DNA COMPLEX SOLUTION CONTAINS 0.01 M DTT AND 0.005 M NAN3, PROTEIN:DNA RATIO IS 1:1.2	Resolution 1.85 Å R-free 0.271
1GU4 Crystal structure of C/EBPBETA BZIP homodimer bound to a high affinity DNA fragment Deposited 2002-01-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 259–336（78 aa） Fragment：BZIP DOMAIN, RESIDUES 259-336 Chain B 259–336（78 aa） Fragment：BZIP DOMAIN, RESIDUES 259-336	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.2 M POTASSIUM CHLORIDE, 0.01 M MAGNESIUM SULFATE, 10.0% V/V PEG 400, 0.05 M MES BUFFER PH 6.0, PROTEIN-DNA COMPLEX CONCENTRATION WAS 12 MG/ML AND CONTAINS 0.01 M DTT, PROTEIN:DNA RATIO WAS 1:1.2. FOR CRYOPROTECTION THE CONCENTRATION OF PEG 400 WAS ADJUSTED TO 36% V/V	Resolution 1.80 Å R-free 0.266
1GU5 Crystal structure of C/EBPBETA BZIP homodimer bound to a DNA fragment from the MIM-1 promoter Deposited 2002-01-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 259–336（78 aa） Fragment：BZIP DOMAIN, RESIDUES 259-336 Chain B 259–336（78 aa） Fragment：BZIP DOMAIN, RESIDUES 259-336	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.08 M MAGNESIUM ACETATE, 15.0% V/V PEG 400, 0.05 M SODIUM CACODYLATE BUFFER PH 6.5, PROTEIN-DNA COMPLEX CONCENTRATION WAS 12 MG/ML WITH ADDITION OF 0.01 M DTT, PROTEIN:DNA RATIO WAS 1:1.2 FOR CRYOPROTECTION THE CONCENTRATION OF PEG 400 WAS ADJUSTED TO 36% V/V	Resolution 2.10 Å R-free 0.277
1H89 CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX2 Deposited 2001-01-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain A 273–336（64 aa） Fragment：RESIDUES 273-336 Chain B 273–336（64 aa） Fragment：RESIDUES 273-336	Not recorded	K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；297 K；0.1 M KCL, 0.05 MGSO4, 4% V/V MPD, 6% V/V GLYCEROL, 0.05 M NA HEPES PH 7.0 AT 24 DEGREES C	Resolution 2.45 Å R-free 0.267
1H8A CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX3 Deposited 2001-01-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain A 259–336（78 aa） Fragment：RESIDUES 259-336 Chain B 259–336（78 aa） Fragment：RESIDUES 259-336	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；297 K；0.04 M MAGNESIUM CHLORIDE, 20% V/V MPD, 0.05 M SODIUM CACODYLATE BUFFER PH 6.0 AT 24 DEGREES C	Resolution 2.23 Å R-free 0.288
1HJB CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN AND C/EBPBETA BZIP HOMODIMER BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER Deposited 2001-01-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain A 259–345（87 aa） Fragment：RESIDUES 259-345 Chain B 259–345（87 aa） Fragment：RESIDUES 259-345	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；297 K；5 MM MGSO4, 3% W/V PEG 4000, 1% V/V DIOXANE, 50 MM MES BUFFER, PH 5.6 AT 24 DEGREES C	Resolution 3.00 Å R-free 0.313
1HJB CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN AND C/EBPBETA BZIP HOMODIMER BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER Deposited 2001-01-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain D 259–345（87 aa） Fragment：RESIDUES 259-345 Chain E 259–345（87 aa） Fragment：RESIDUES 259-345	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；297 K；5 MM MGSO4, 3% W/V PEG 4000, 1% V/V DIOXANE, 50 MM MES BUFFER, PH 5.6 AT 24 DEGREES C	Resolution 3.00 Å R-free 0.313
1IO4 CRYSTAL STRUCTURE OF RUNX-1/AML1/CBFALPHA RUNT DOMAIN-CBFBETA CORE DOMAIN HETERODIMER AND C/EBPBETA BZIP HOMODIMER BOUND TO A DNA FRAGMENT FROM THE CSF-1R PROMOTER Deposited 2001-01-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 259–336（78 aa） Fragment：BZIP DOMAIN Chain B 259–336（78 aa） Fragment：BZIP DOMAIN	Not recorded	AU GOLD ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；297 K；0.2 M potassium chloride, 0.01 M magnesium chloride, 0.01 M DTT, 4.5% V/V PEG 8000, 1% V/V glycerol, 1% V/V MPD, 0.05 M MES buffer pH 5.6, pH 5.60, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 3.00 Å R-free 0.299
2E42 Crystal structure of C/EBPbeta Bzip homodimer V285A mutant bound to A High Affinity DNA fragment Deposited 2006-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 259–336（78 aa） Fragment：residues 259-336 Chain B 259–336（78 aa） Fragment：residues 259-336	Mutation：V285A Mutation：V285A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；magnesium chloride, MES, PEG400, PH 6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K	Resolution 1.80 Å R-free 0.252
2E43 Crystal structure of C/EBPbeta Bzip homodimer K269A mutant bound to A High Affinity DNA fragment Deposited 2006-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 259–336（78 aa） Fragment：residues 259-336 Chain B 259–336（78 aa） Fragment：residues 259-336	Mutation：K269A Mutation：K269A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；magnesium chloride, Tris-Hcl, PEG4000, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K	Resolution 2.10 Å R-free 0.259
6MG1 C-terminal bZIP domain of human C/EBPbeta with 16bp Methylated Oligonucleotide Containing Consensus Recognition Sequence-C2 Crystal Form Deposited 2018-09-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 246–321（76 aa） Chain B 246–321（76 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；0.2 M sodium chloride, 0.1 M BIS-TRIS pH 6.5, 25% (w/v) polyethylene glycol 3350	Resolution 1.75 Å R-free 0.250
6MG2 C-terminal bZIP domain of human C/EBPbeta with 16bp Methylated Oligonucleotide Containing Consensus Recognition Sequence-C2221 Crystal Form Deposited 2018-09-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 246–321（76 aa） Chain B 246–321（76 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；0.1 M sodium acetate trihydrate pH 7.0, 12% (w/v) polyethylene glycol 3350	Resolution 1.93 Å R-free 0.210
6MG3 V285A Mutant of the C-terminal bZIP domain of human C/EBPbeta with 16bp Methylated Oligonucleotide Containing Consensus Recognition Sequence Deposited 2018-09-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 246–321（76 aa） Chain B 246–321（76 aa）	Mutation：V285A Mutation：V285A	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；0.1 M sodium acetate trihydrate pH 7.0, 12% (w/v) polyethylene glycol 3350	Resolution 2.05 Å R-free 0.249
7L4V C-terminal bZIP domain of human C/EBPbeta Bound to DNA with Consensus Recognition with GT Mismatch Deposited 2020-12-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 246–321（76 aa） Chain B 246–321（76 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；292 K；50 mM ammonium sulfate, 50 mM BIS-TRIS pH 6.5, 30% (v/v) pentaerythritol ethoxylate (15/4 EO/OH)	Resolution 1.75 Å R-free 0.221
7UPZ Structural basis for cell type specific DNA binding of C/EBPbeta: the case of cell cycle inhibitor p15INK4b promoter Deposited 2022-04-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 257–336（80 aa） Fragment：UNP residues 257-336 Chain B 257–336（80 aa） Fragment：UNP residues 257-336	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；100 mM potassium chloride, 10 mM magnesium chloride, 50 mM MES, pH 6.0, 10% v/v PEG400, 5% v/v glycerol	Resolution 2.49 Å R-free 0.264
8K8D Crystal structure of C/EBPbeta BZIP domain bound to a high affinity DNA Deposited 2023-07-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 259–336（78 aa） Chain B 259–336（78 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.02 M Calcium chloride dihydrate,0.1 M Sodium acetate trihydrate pH 4.6 and 20% v/v 2-Propanol	Resolution 2.20 Å R-free 0.292

15 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CEBB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–78； UniProt 259–336 Author chain B； PDBConstruct 1–78； UniProt 259–336

MYB PROTO-ONCOGENE PROTEIN

MUS MUSCULUS

UniProt P06876

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 Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain C； UniProt 35–193	Fragment：RESIDUES 35-193 Mutation：YES	CCAAT/ENHANCER BINDING PROTEIN BETA × 2 （P17676） ;DNA(5'-(GPAPTPGPTPGPGPCPGPCPAP APTPCPCPTPTPAPAPCPGPGPAPCPTPG)-3') ; × 1 ;DNA(5'-(CPCPAPGPTPCPCPGPTPTPAP APGPGPAPTPTPGPCPGPCPCPAPCPAPT)-3') ; × 1 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

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 1H88	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 oligomeric state 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 oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 oligomeric state 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
1IDY STRUCTURE OF MYB TRANSFORMING PROTEIN, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1996-08-15	Different construct Different mutation/modification Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–159； UniProt 35–193

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	1h88
Deposition date deposition_date	2001-01-29
Structure title title	CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX1
Keywords keywords	TRANSCRIPTION-DNA COMPLEX, TRANSCRIPTION REGULATION, BZIP, PROTO-ONCOGENE, MYB, C-MYB, C/EBP; TRANSCRIPTION/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	31.85 Å
Radius of gyration Rg (electron density) rg_electron	33.46 Å
Forward intensity I(0) i0	63814600.00
Molecular weight molecular_weight	51368.0 kDa
Excluded volume excluded_volume	59452 Å³
Envelope volume envelope_volume	91717 Å³
Hydration-shell volume shell_volume	25564 Å³
Envelope diameter envelope_diameter	129.9 Å
Shell Rg shell_rg	35.44 Å
Envelope Rg envelope_rg	34.02 Å
Shape Rg shape_rg	33.51 Å
Total Rg total_rg	33.48 Å
Total atoms total_atoms	3551
Residues n_residues	345
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	126.6 Å
Rg (real space) rg_real	32.27 Å
Rg uncertainty (real space) rg_real_error	1.80 Å
I(0) (real space) i0_real	6.3810e+07
I(0) uncertainty (real space) i0_real_error	1.2010e+06
Rg (reciprocal space) rg_reciprocal	32.09 Å
I(0) (reciprocal space) i0_reciprocal	63810000.0000
Solution quality estimate total_estimate	0.7561
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	27.9 Å
Skewness Skewness skewness	0.550
Kurtosis Kurtosis kurtosis	-0.132
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3594000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.498; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.356; Smooth: 0.974

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	CCAAT/ENHANCER BINDING PROTEIN BETA
Molecular weight formula_weight	9381.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3576

VKSKAKKTVDKHSDEYKIRRERNNIAVRKSRDKAKMRNLETQHKVLELTAENERLQKKVEQLSRELSTLRNLFKQLPE

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 2 Entity 2 polymer

Description description	MYB PROTO-ONCOGENE PROTEIN
Molecular weight formula_weight	19173.1 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGHLGKTRWTREEDEKLKKLVEQNGTDDWKVIANYLPNRTDVQCQHRWQKVLNPELIKGPWTKEEDQRVIKLVQKYGPKRWSVIAKHLKGRIGKQCRERWHNHLNPEVKKTSWTEEEDRIIYQAHKRLGNRWAEIAKLLPGRTDNAIKNHWNSTMRRKV

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	HOUSE MOUSE
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 polymer

Description description	;DNA(5'-(GPAPTPGPTPGPGPCPGPCPAP APTPCPCPTPTPAPAPCPGPGPAPCPTPG)-3') ;
Molecular weight formula_weight	8028.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

GATGTGGCGCAATCCTTAACGGACTG

Entity 4 Entity 4 polymer

Description description	;DNA(5'-(CPCPAPGPTPCPCPGPTPTPAP APGPGPAPTPTPGPCPGPCPCPAPCPAPT)-3') ;
Molecular weight formula_weight	7948.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

CCAGTCCGTTAAGGATTGCGCCACAT

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	25

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1h88a_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.3 — Leucine zipper domain
Family Family family	h.1.3.1 — Leucine zipper domain

Domain ID domain_id	d1h88b_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.3 — Leucine zipper domain
Family Family family	h.1.3.1 — Leucine zipper domain

Domain ID domain_id	d1h88c1
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	d1h88c2
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	d1h88c3
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 (5 domains)

Domain ID domain_id	1h88A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	1h88B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	1h88C01
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	1h88C02
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	1h88C03
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	41.735 Å
Unit-cell length b length_b	156.966 Å
Unit-cell length c length_c	55.868 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.16 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	19.870 Å
R factor r_factor	0.2220
R_work r_work	0.2220
R_free r_free	0.2770

fit	/app/data/saxs_computation/h8/1h88/1h88.fit
pddf	/app/data/pr_computation/h8/1h88/1h88.pr.out
profile	/app/data/saxs_computation/h8/1h88/1h88.dat

CRYSTAL STRUCTURE OF TERNARY PROTEIN-DNA COMPLEX1

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

CCAAT/ENHANCER BINDING PROTEIN BETA

State in the Current Structure

Other States of the Same Protein in the Database

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

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)