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- PDB-1am9: HUMAN SREBP-1A BOUND TO LDL RECEPTOR PROMOTER -

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Basic information

Entry
Database: PDB / ID: 1am9
TitleHUMAN SREBP-1A BOUND TO LDL RECEPTOR PROMOTER
Components
  • DNA (5'-D(*CP*AP*TP*GP*AP*GP*AP*TP*CP*AP*CP*CP*CP*CP*AP*CP*T P*GP*CP*AP*A)-3')
  • DNA (5'-D(*TP*TP*GP*CP*AP*GP*TP*GP*GP*GP*GP*TP*GP*AP*TP*CP*T )-3')
  • PROTEIN (STEROL REGULATORY ELEMENT BINDING PROTEIN 1A)
KeywordsTRANSCRIPTION/DNA / STEROL REGULATORY ELEMENT BINDING PROTEIN / BASIC-HELIX-LOOP-HELIX-LEUCINE ZIPPER / SREBP / TRANSCRIPTION FACTOR / COMPLEX (TRANSCRIPTION REGULATION-DNA) / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


regulation of heart rate by chemical signal / lipid localization / : / sterol response element binding / regulation of protein targeting to mitochondrion / regulation of cholesterol biosynthetic process / regulation of lipid storage / : / SREBP signaling pathway / response to xenobiotic stimulus => GO:0009410 ...regulation of heart rate by chemical signal / lipid localization / : / sterol response element binding / regulation of protein targeting to mitochondrion / regulation of cholesterol biosynthetic process / regulation of lipid storage / : / SREBP signaling pathway / response to xenobiotic stimulus => GO:0009410 / regulation of autophagy of mitochondrion / regulation of fatty acid metabolic process / positive regulation of triglyceride biosynthetic process / chromatin => GO:0000785 / positive regulation of cholesterol biosynthetic process / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / Regulation of cholesterol biosynthesis by SREBP (SREBF) / response to glucagon / response to food / lipid biosynthetic process / cellular response to fatty acid / response to lipid / fat cell differentiation / negative regulation of insulin secretion / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to glucose / response to retinoic acid / response to cAMP / RORA activates gene expression / cellular response to starvation / cholesterol metabolic process / Activation of gene expression by SREBF (SREBP) / response to progesterone / RNA polymerase II transcription regulatory region sequence-specific DNA binding / lung development / mRNA transcription by RNA polymerase II / regulation of protein stability / ER to Golgi transport vesicle membrane / lipid metabolic process / PPARA activates gene expression / positive regulation of miRNA transcription / Transcriptional regulation of white adipocyte differentiation / circadian rhythm / nuclear receptor activity / sequence-specific double-stranded DNA binding / insulin receptor signaling pathway / nuclear envelope / DNA-binding transcription activator activity, RNA polymerase II-specific / response to ethanol / membrane => GO:0016020 / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / Golgi membrane / chromatin binding / protein-containing complex binding / endoplasmic reticulum membrane / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
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) / Sterol regulatory element-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsParraga, A. / Burley, S.K.
CitationJournal: Structure / Year: 1998
Title: Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 A resolution.
Authors: Parraga, A. / Bellsolell, L. / Ferre-D'Amare, A.R. / Burley, S.K.
History
DepositionJun 25, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 10, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: DNA (5'-D(*TP*TP*GP*CP*AP*GP*TP*GP*GP*GP*GP*TP*GP*AP*TP*CP*T )-3')
F: DNA (5'-D(*CP*AP*TP*GP*AP*GP*AP*TP*CP*AP*CP*CP*CP*CP*AP*CP*T P*GP*CP*AP*A)-3')
G: DNA (5'-D(*TP*TP*GP*CP*AP*GP*TP*GP*GP*GP*GP*TP*GP*AP*TP*CP*T )-3')
H: DNA (5'-D(*CP*AP*TP*GP*AP*GP*AP*TP*CP*AP*CP*CP*CP*CP*AP*CP*T P*GP*CP*AP*A)-3')
A: PROTEIN (STEROL REGULATORY ELEMENT BINDING PROTEIN 1A)
B: PROTEIN (STEROL REGULATORY ELEMENT BINDING PROTEIN 1A)
C: PROTEIN (STEROL REGULATORY ELEMENT BINDING PROTEIN 1A)
D: PROTEIN (STEROL REGULATORY ELEMENT BINDING PROTEIN 1A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,32210
Polymers61,2738
Non-polymers492
Water5,386299
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.630, 94.630, 459.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: DNA chain DNA (5'-D(*TP*TP*GP*CP*AP*GP*TP*GP*GP*GP*GP*TP*GP*AP*TP*CP*T )-3')


Mass: 5289.417 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*AP*TP*GP*AP*GP*AP*TP*CP*AP*CP*CP*CP*CP*AP*CP*T P*GP*CP*AP*A)-3')


Mass: 6361.140 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Protein
PROTEIN (STEROL REGULATORY ELEMENT BINDING PROTEIN 1A) / SREBP-1A


Mass: 9492.990 Da / Num. of mol.: 4 / Fragment: DNA BINDING DOMAIN / Mutation: C404S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P36956
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 74.21 %
Description: THE CCD DETECTOR WAS OFFSET IN TWO DIRECTIONS DURING DATA COLLECTION
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: PROTEIN WAS CRYSTALLIZED FROM 20 % MPD, 100 MM KCL, 20 MM MGCL2, 100 MM HEPES, PH 5.6, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2KCL11
3MGCL211
4TRIS-HCL11
5WATER12
6MPD12
7KCL12
8MGCL212
9MES12
10WATER13
11KCL13
12MGCL213
13MES13
14PEG 400013
15MPD13
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.5 mMprotein1drop
2150 mM1reservoirKCl
320 mM1reservoirMgCl2
4100 mMMES1reservoirpH5.6
510 %MPD1reservoir
61
71
81
91
101
111
121
131
141
151

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1
DetectorDetector: CCD / Date: Oct 24, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 48155 / % possible obs: 87 % / Observed criterion σ(I): 0 / Redundancy: 12 % / Rsym value: 0.071 / Net I/σ(I): 36
Reflection shellResolution: 2.3→2.48 Å / Redundancy: 4 % / Rsym value: 0.34 / % possible all: 52.4
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. all: 633236 / % possible obs: 86.9 % / Rmerge(I) obs: 0.071

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MAX-DNA STRUCTURE

Resolution: 2.3→6 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.278 4306 10 %RANDOM
Rwork0.219 ---
obs0.219 43209 85 %-
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2441 1546 14 287 4288
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.68
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.36
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: 2.3 Å / Lowest resolution: 6 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.77
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36

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