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- PDB-1an4: STRUCTURE AND FUNCTION OF THE B/HLH/Z DOMAIN OF USF -

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Basic information

Entry
Database: PDB / ID: 1an4
TitleSTRUCTURE AND FUNCTION OF THE B/HLH/Z DOMAIN OF USF
Components
  • DNA (5'-D(*CP*AP*CP*CP*CP*GP*GP*TP*CP*AP*CP*GP*TP*GP*GP*CP*C P*TP*AP*CP*A)-3')
  • DNA (5'-D(*GP*TP*GP*TP*AP*GP*GP*CP*CP*AP*CP*GP*TP*GP*AP*CP*C P*GP*GP*GP*T)-3')
  • PROTEIN (UPSTREAM STIMULATORY FACTOR)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / OVERHANGING BASE / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


carbon catabolite regulation of transcription / regulation of transcription from RNA polymerase II promoter by glucose / late viral transcription / positive regulation of transcription from RNA polymerase II promoter by glucose / bHLH transcription factor binding / chromatin => GO:0000785 / lipid homeostasis / negative regulation of fibrinolysis / response to UV / histone deacetylase binding ...carbon catabolite regulation of transcription / regulation of transcription from RNA polymerase II promoter by glucose / late viral transcription / positive regulation of transcription from RNA polymerase II promoter by glucose / bHLH transcription factor binding / chromatin => GO:0000785 / lipid homeostasis / negative regulation of fibrinolysis / response to UV / histone deacetylase binding / cellular response to insulin stimulus / glucose metabolic process / sequence-specific double-stranded DNA binding / glucose homeostasis / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / protein-containing complex binding / regulation of transcription by RNA polymerase II / protein kinase binding / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / DNA (> 10) / Upstream stimulatory factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsFerre-D'Amare, A.R. / Pognonec, P. / Roeder, R.G. / Burley, S.K.
CitationJournal: EMBO J. / Year: 1994
Title: Structure and function of the b/HLH/Z domain of USF.
Authors: Ferre-D'Amare, A.R. / Pognonec, P. / Roeder, R.G. / Burley, S.K.
History
DepositionMar 15, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Category: reflns / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.4Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*CP*AP*CP*CP*CP*GP*GP*TP*CP*AP*CP*GP*TP*GP*GP*CP*C P*TP*AP*CP*A)-3')
D: DNA (5'-D(*GP*TP*GP*TP*AP*GP*GP*CP*CP*AP*CP*GP*TP*GP*AP*CP*C P*GP*GP*GP*T)-3')
A: PROTEIN (UPSTREAM STIMULATORY FACTOR)
B: PROTEIN (UPSTREAM STIMULATORY FACTOR)


Theoretical massNumber of molelcules
Total (without water)28,1974
Polymers28,1974
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-39 kcal/mol
Surface area16070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.600, 54.700, 44.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*CP*AP*CP*CP*CP*GP*GP*TP*CP*AP*CP*GP*TP*GP*GP*CP*C P*TP*AP*CP*A)-3')


Mass: 6369.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#2: DNA chain DNA (5'-D(*GP*TP*GP*TP*AP*GP*GP*CP*CP*AP*CP*GP*TP*GP*AP*CP*C P*GP*GP*GP*T)-3') / UPSTREAM STIMULATORY FACTOR 1


Mass: 6520.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#3: Protein PROTEIN (UPSTREAM STIMULATORY FACTOR)


Mass: 7653.597 Da / Num. of mol.: 2
Fragment: FRAGMENT:B/HLH DNA BINDING DOMAIN MUTATION:R196M, C229S, C248S
Mutation: R196M, C229S, C248S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Bacteria (eubacteria) / Keywords: B/HLH DNA BINDING DOMAIN / References: UniProt: P22415

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.75
Details: pH 4.75, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2PEG 40011
3GLYCEROL11
4KCL11
5MGCL211
6CD ACETATE11
7NA ACETATE11
8WATER12
9PEG 40012
10GLYCEROL12
11KCL12
12MGCL212
13CD ACETATE12
14NA ACETATE12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.4 mMDNA1drop
2100 mM1dropKCl
310 mMHEPES1drop
415 %PEG4001reservoir
515 %glycerol1reservoir
6100 mM1reservoirKCl
72.8 mM1reservoirMgCl2
81.4 mMCd(II) acetate1reservoir
9100 mMsodium acetate1reservoir
101
111
121
131
141

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Data collection

DiffractionMean temperature: 253 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1
DetectorDetector: IMAGE PLATE / Date: Jun 1, 1993
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→15 Å / Num. all: 32049 / Num. obs: 6038 / % possible obs: 77.2 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 14.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 1.5 % / % possible all: 49.3
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 15 Å / % possible obs: 76.4 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Num. measured all: 32049
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 49.3 % / Redundancy: 1.5 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.9→6 Å / Rfactor Rwork: 0.236 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1068 855 0 0 1923
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 6 Å / Num. reflection obs: 5096 / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 3.05

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