1AM9

HUMAN SREBP-1A BOUND TO LDL RECEPTOR PROMOTER

> Summary

Summary for 1AM9

DescriptorSTEROL REGULATORY ELEMENT BINDING(STRE)/DNA COMPLEX
Functional Keywordssterol regulatory element binding protein, basic-helix-loop-helix-leucine zipper, srebp, transcription factor, complex (transcription regulation-dna), transcription-dna complex, transcription/dna
Biological sourceHomo sapiens (human)
Cellular locationEndoplasmic reticulum membrane; Multi-pass membrane protein. Processed sterol regulatory element-binding protein 1: Nucleus P36956
Total number of polymer chains8
Total molecular weight61322.25
Authors
Parraga, A.,Burley, S.K. (deposition date: 1997-06-25, release date: 1998-07-10, modification date: 2009-02-24)
Primary citation
Parraga, A.,Bellsolell, L.,Ferre-D'Amare, A.R.,Burley, S.K.
Co-crystal structure of sterol regulatory element binding protein 1a at 2.3 A resolution.
Structure, 6:661-672, 1998
PubMed: 9634703
DOI: 10.1016/S0969-2126(98)00067-7
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.3 Å)
?

Structure validation

ClashscoreRamachandran outliersSidechain outliers151.0%2.4%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1am9
no rotation
Molmil generated image of 1am9
rotated about x axis by 90°
Molmil generated image of 1am9
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
E, GDNA (5'-D(*TP*TP*GP*CP*AP*GP*TP*GP*GP*GP*GP*TP*GP*AP*TP*CP*T )-3')polymer175289.52
F, HDNA (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')polymer216361.22
A, B, C, DPROTEIN (STEROL REGULATORY ELEMENT BINDING PROTEIN 1A)polymer829493.14
UniProt (P36956)
Pfam (PF00010)
Homo sapiens (human)@PDBjSREBP-1A
MAGNESIUM IONnon-polymer24.32
waterwater18.0299

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains8
Total molecular weight61273.6
Non-Polymers*Number of molecules2
Total molecular weight48.6
All*Total molecular weight61322.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.3 Å)

Cell axes94.63094.630459.100
Cell angles90.0090.00120.00
SpacegroupP 61 2 2
Resolution limits6.00 - 2.30
the highest resolution shell value -
R-factor0.219
R-work0.21900
R-free0.27800
RMSD bond length0.013
RMSD bond angle1.680 (23.770*)

Data Collection Statistics

Resolution limits20.00 - 2.30
the highest resolution shell value -
Number of reflections48155
Rmerge_l_obs0.071*
Completeness87.0 (86.9*)
Redundancy12
the highest resolution shell value4
I/sigma(I)0

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP5.6unknown*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
111WATER
211KCL
311MGCL2
411TRIS-HCL
512WATER
612MPD
712KCL
812MGCL2
912MES
1013WATER
1113KCL
1213MGCL2
1313MES
1413PEG 4000
1513MPD
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11dropprotein0.5 (mM)
21reservoir150 (mM)
31reservoir20 (mM)
41reservoirMES100 (mM)pH5.6
51reservoirMPD10 (%)
Annotated Information is extracted from Literature Info*

> Functional details

?

Functional Information from GO Data

ChainGOidnamespacecontents
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0005783cellular_componentendoplasmic reticulum
A0005789cellular_componentendoplasmic reticulum membrane
A0012507cellular_componentER to Golgi transport vesicle membrane
A0000139cellular_componentGolgi membrane
A0016021cellular_componentintegral component of membrane
A0005635cellular_componentnuclear envelope
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0043234cellular_componentprotein complex
A0003682molecular_functionchromatin binding
A0003677molecular_functionDNA binding
A0000978molecular_functionRNA polymerase II core promoter proximal region sequence-specific DNA binding
A0032810molecular_functionsterol response element binding
A0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
A0001077molecular_functiontranscriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
A0007568biological_processaging
A0071398biological_processcellular response to fatty acid
A0009267biological_processcellular response to starvation
A0008203biological_processcholesterol metabolic process
A0007623biological_processcircadian rhythm
A0045444biological_processfat cell differentiation
A0008286biological_processinsulin receptor signaling pathway
A0008610biological_processlipid biosynthetic process
A0006629biological_processlipid metabolic process
A0030324biological_processlung development
A0042789biological_processmRNA transcription from RNA polymerase II promoter
A0046676biological_processnegative regulation of insulin secretion
A0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
A0045542biological_processpositive regulation of cholesterol biosynthetic process
A0031065biological_processpositive regulation of histone deacetylation
A0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
A0010867biological_processpositive regulation of triglyceride biosynthetic process
A0019217biological_processregulation of fatty acid metabolic process
A0003062biological_processregulation of heart rate by chemical signal
A1903146biological_processregulation of mitophagy
A0031647biological_processregulation of protein stability
A1903214biological_processregulation of protein targeting to mitochondrion
A0006357biological_processregulation of transcription from RNA polymerase II promoter
A0051591biological_processresponse to cAMP
A0042493biological_processresponse to drug
A0032094biological_processresponse to food
A0033762biological_processresponse to glucagon
A0009749biological_processresponse to glucose
A0032570biological_processresponse to progesterone
A0032526biological_processresponse to retinoic acid
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0005783cellular_componentendoplasmic reticulum
B0005789cellular_componentendoplasmic reticulum membrane
B0012507cellular_componentER to Golgi transport vesicle membrane
B0000139cellular_componentGolgi membrane
B0016021cellular_componentintegral component of membrane
B0005635cellular_componentnuclear envelope
B0005654cellular_componentnucleoplasm
B0005634cellular_componentnucleus
B0043234cellular_componentprotein complex
B0003682molecular_functionchromatin binding
B0003677molecular_functionDNA binding
B0000978molecular_functionRNA polymerase II core promoter proximal region sequence-specific DNA binding
B0032810molecular_functionsterol response element binding
B0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
B0001077molecular_functiontranscriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
B0007568biological_processaging
B0071398biological_processcellular response to fatty acid
B0009267biological_processcellular response to starvation
B0008203biological_processcholesterol metabolic process
B0007623biological_processcircadian rhythm
B0045444biological_processfat cell differentiation
B0008286biological_processinsulin receptor signaling pathway
B0008610biological_processlipid biosynthetic process
B0006629biological_processlipid metabolic process
B0030324biological_processlung development
B0042789biological_processmRNA transcription from RNA polymerase II promoter
B0046676biological_processnegative regulation of insulin secretion
B0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
B0045542biological_processpositive regulation of cholesterol biosynthetic process
B0031065biological_processpositive regulation of histone deacetylation
B0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
B0010867biological_processpositive regulation of triglyceride biosynthetic process
B0019217biological_processregulation of fatty acid metabolic process
B0003062biological_processregulation of heart rate by chemical signal
B1903146biological_processregulation of mitophagy
B0031647biological_processregulation of protein stability
B1903214biological_processregulation of protein targeting to mitochondrion
B0006357biological_processregulation of transcription from RNA polymerase II promoter
B0051591biological_processresponse to cAMP
B0042493biological_processresponse to drug
B0032094biological_processresponse to food
B0033762biological_processresponse to glucagon
B0009749biological_processresponse to glucose
B0032570biological_processresponse to progesterone
B0032526biological_processresponse to retinoic acid
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0005783cellular_componentendoplasmic reticulum
C0005789cellular_componentendoplasmic reticulum membrane
C0012507cellular_componentER to Golgi transport vesicle membrane
C0000139cellular_componentGolgi membrane
C0016021cellular_componentintegral component of membrane
C0005635cellular_componentnuclear envelope
C0005654cellular_componentnucleoplasm
C0005634cellular_componentnucleus
C0043234cellular_componentprotein complex
C0003682molecular_functionchromatin binding
C0003677molecular_functionDNA binding
C0000978molecular_functionRNA polymerase II core promoter proximal region sequence-specific DNA binding
C0032810molecular_functionsterol response element binding
C0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
C0001077molecular_functiontranscriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
C0007568biological_processaging
C0071398biological_processcellular response to fatty acid
C0009267biological_processcellular response to starvation
C0008203biological_processcholesterol metabolic process
C0007623biological_processcircadian rhythm
C0045444biological_processfat cell differentiation
C0008286biological_processinsulin receptor signaling pathway
C0008610biological_processlipid biosynthetic process
C0006629biological_processlipid metabolic process
C0030324biological_processlung development
C0042789biological_processmRNA transcription from RNA polymerase II promoter
C0046676biological_processnegative regulation of insulin secretion
C0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
C0045542biological_processpositive regulation of cholesterol biosynthetic process
C0031065biological_processpositive regulation of histone deacetylation
C0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
C0010867biological_processpositive regulation of triglyceride biosynthetic process
C0019217biological_processregulation of fatty acid metabolic process
C0003062biological_processregulation of heart rate by chemical signal
C1903146biological_processregulation of mitophagy
C0031647biological_processregulation of protein stability
C1903214biological_processregulation of protein targeting to mitochondrion
C0006357biological_processregulation of transcription from RNA polymerase II promoter
C0051591biological_processresponse to cAMP
C0042493biological_processresponse to drug
C0032094biological_processresponse to food
C0033762biological_processresponse to glucagon
C0009749biological_processresponse to glucose
C0032570biological_processresponse to progesterone
C0032526biological_processresponse to retinoic acid
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0005783cellular_componentendoplasmic reticulum
D0005789cellular_componentendoplasmic reticulum membrane
D0012507cellular_componentER to Golgi transport vesicle membrane
D0000139cellular_componentGolgi membrane
D0016021cellular_componentintegral component of membrane
D0005635cellular_componentnuclear envelope
D0005654cellular_componentnucleoplasm
D0005634cellular_componentnucleus
D0043234cellular_componentprotein complex
D0003682molecular_functionchromatin binding
D0003677molecular_functionDNA binding
D0000978molecular_functionRNA polymerase II core promoter proximal region sequence-specific DNA binding
D0032810molecular_functionsterol response element binding
D0003700molecular_functiontranscription factor activity, sequence-specific DNA binding
D0001077molecular_functiontranscriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
D0007568biological_processaging
D0071398biological_processcellular response to fatty acid
D0009267biological_processcellular response to starvation
D0008203biological_processcholesterol metabolic process
D0007623biological_processcircadian rhythm
D0045444biological_processfat cell differentiation
D0008286biological_processinsulin receptor signaling pathway
D0008610biological_processlipid biosynthetic process
D0006629biological_processlipid metabolic process
D0030324biological_processlung development
D0042789biological_processmRNA transcription from RNA polymerase II promoter
D0046676biological_processnegative regulation of insulin secretion
D0000122biological_processnegative regulation of transcription from RNA polymerase II promoter
D0045542biological_processpositive regulation of cholesterol biosynthetic process
D0031065biological_processpositive regulation of histone deacetylation
D0045944biological_processpositive regulation of transcription from RNA polymerase II promoter
D0010867biological_processpositive regulation of triglyceride biosynthetic process
D0019217biological_processregulation of fatty acid metabolic process
D0003062biological_processregulation of heart rate by chemical signal
D1903146biological_processregulation of mitophagy
D0031647biological_processregulation of protein stability
D1903214biological_processregulation of protein targeting to mitochondrion
D0006357biological_processregulation of transcription from RNA polymerase II promoter
D0051591biological_processresponse to cAMP
D0042493biological_processresponse to drug
D0032094biological_processresponse to food
D0033762biological_processresponse to glucagon
D0009749biological_processresponse to glucose
D0032570biological_processresponse to progesterone
D0032526biological_processresponse to retinoic acid
?

Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC16BINDING SITE FOR RESIDUE MG C 2001
ChainResidue
DHOH2003
DHOH2004
DHOH2005
DHOH2006
DHOH2007
DHOH2008

AC26BINDING SITE FOR RESIDUE MG B 2002
ChainResidue
AHOH2009
AHOH2012
AHOH2013
BHOH2010
BHOH2011
BHOH2014

?

Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
?

Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
?

Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI41Basic motif.
ChainResidueDetails
ANA*

SWS_FT_FI91Basic motif.
ChainResidueDetails
BNA*

SWS_FT_FI141Basic motif.
ChainResidueDetails
CNA*

SWS_FT_FI191Basic motif.
ChainResidueDetails
DNA*

?

Catalytic Information from CSA

site_idNumber of ResiduesDetails
?

Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

PDBj@FacebookPDBj@TwitterwwPDBwwPDB FoundationEM DataBank

Copyright © 2013-2016 Protein Data Bank Japan