1W1W

Sc Smc1hd:Scc1-C complex, ATPgS

> Summary

Summary for 1W1W

DescriptorSTRUCTURAL MAINTENANCE OF CHROMOSOME 1, SISTER CHROMATID COHESION PROTEIN 1
Functional Keywordscohesin, chromosome segregation, cell adhesion, kleisin, mitosis, cell cycle
Biological sourceSACCHAROMYCES CEREVISIAE (BAKER'S YEAST)
Cellular locationNucleus P32908 Q12158
Total number of polymer chains8
Total molecular weight252599.44
Authors
Haering, C.,Nasmyth, K.,Lowe, J. (deposition date: 2004-06-24, release date: 2004-09-30, modification date: 2013-02-06)
Primary citation
Haering, C.,Schoffnegger, D.,Nishino, T.,Helmhart, W.,Nasmyth, K.,Lowe, J.
Structure and Stability of Cohesin'S Smc1-Kleisin Interaction
Mol.Cell, 15:951-, 2004
PubMed: 15383284
DOI: 10.1016/J.MOLCEL.2004.08.030
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.9 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.239242.2%7.9%8.0%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1w1w
no rotation
Molmil generated image of 1w1w
rotated about x axis by 90°
Molmil generated image of 1w1w
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 1w1w
no rotation
Molmil generated image of 1w1w
rotated about x axis by 90°
Molmil generated image of 1w1w
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (1w1w.pdb1.gz [69.53 KB])
Coordinate files for Biological unit (1w1w.pdb2.gz [60.65 KB])
Coordinate files for Biological unit (1w1w.pdb3.gz [69.81 KB])
Coordinate files for Biological unit (1w1w.pdb4.gz [69.22 KB])
Coordinate files for Biological unit (1w1w.pdb5.gz [124.47 KB])
Coordinate files for Biological unit (1w1w.pdb6.gz [133.55 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, B, C, DSTRUCTURAL MAINTENANCE OF CHROMOSOME 1polymer43048855.64
UniProt (P32908)
Pfam (PF02463)
SACCHAROMYCES CEREVISIAE (BAKER'S YEAST)@PDBjSMC1, DA-BOX PROTEIN SMC1
E, F, G, HSISTER CHROMATID COHESION PROTEIN 1polymer12113746.74
UniProt (Q12158)
Pfam (PF04824)
SACCHAROMYCES CEREVISIAE (BAKER'S YEAST)@PDBjSCC1
MAGNESIUM IONnon-polymer24.34
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTERnon-polymer523.24

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains8
Total molecular weight250409.2
Non-Polymers*Number of molecules8
Total molecular weight2190.2
All*Total molecular weight252599.4
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.9 Å)

Cell axes138.465138.465284.074
Cell angles90.0090.0090.00
SpacegroupP 43 21 2
Resolution limits50.00 - 2.90
the highest resolution shell value2.920 - 2.900
R-factor0.2417
R-work0.24170
the highest resolution shell value0.397
R-free0.27490
the highest resolution shell value0.394
RMSD bond length0.008
RMSD bond angle1.456

Data Collection Statistics

Resolution limits57.00 - 2.90
the highest resolution shell value -
Number of reflections59522
Rmerge_l_obs0.080
the highest resolution shell value0.460
Completeness99.0
Redundancy6
the highest resolution shell value5.6
I/sigma(I)0

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
E0000775cellular_componentchromosome, centromeric region
E0000794cellular_componentcondensed nuclear chromosome
E0005739cellular_componentmitochondrion
E0034990cellular_componentnuclear mitotic cohesin complex
E0005634cellular_componentnucleus
E0003682molecular_functionchromatin binding
E0006915biological_processapoptotic process
E0051301biological_processcell division
E0006974biological_processcellular response to DNA damage stimulus
E0006268biological_processDNA unwinding involved in DNA replication
E0006302biological_processdouble-strand break repair
E0034087biological_processestablishment of mitotic sister chromatid cohesion
E0007076biological_processmitotic chromosome condensation
E0006473biological_processprotein acetylation
E1990414biological_processreplication-born double-strand break repair via sister chromatid exchange
F0000775cellular_componentchromosome, centromeric region
F0000794cellular_componentcondensed nuclear chromosome
F0005739cellular_componentmitochondrion
F0034990cellular_componentnuclear mitotic cohesin complex
F0005634cellular_componentnucleus
F0003682molecular_functionchromatin binding
F0006915biological_processapoptotic process
F0051301biological_processcell division
F0006974biological_processcellular response to DNA damage stimulus
F0006268biological_processDNA unwinding involved in DNA replication
F0006302biological_processdouble-strand break repair
F0034087biological_processestablishment of mitotic sister chromatid cohesion
F0007076biological_processmitotic chromosome condensation
F0006473biological_processprotein acetylation
F1990414biological_processreplication-born double-strand break repair via sister chromatid exchange
G0000775cellular_componentchromosome, centromeric region
G0000794cellular_componentcondensed nuclear chromosome
G0005739cellular_componentmitochondrion
G0034990cellular_componentnuclear mitotic cohesin complex
G0005634cellular_componentnucleus
G0003682molecular_functionchromatin binding
G0006915biological_processapoptotic process
G0051301biological_processcell division
G0006974biological_processcellular response to DNA damage stimulus
G0006268biological_processDNA unwinding involved in DNA replication
G0006302biological_processdouble-strand break repair
G0034087biological_processestablishment of mitotic sister chromatid cohesion
G0007076biological_processmitotic chromosome condensation
G0006473biological_processprotein acetylation
G1990414biological_processreplication-born double-strand break repair via sister chromatid exchange
H0000775cellular_componentchromosome, centromeric region
H0000794cellular_componentcondensed nuclear chromosome
H0005739cellular_componentmitochondrion
H0034990cellular_componentnuclear mitotic cohesin complex
H0005634cellular_componentnucleus
H0003682molecular_functionchromatin binding
H0006915biological_processapoptotic process
H0051301biological_processcell division
H0006974biological_processcellular response to DNA damage stimulus
H0006268biological_processDNA unwinding involved in DNA replication
H0006302biological_processdouble-strand break repair
H0034087biological_processestablishment of mitotic sister chromatid cohesion
H0007076biological_processmitotic chromosome condensation
H0006473biological_processprotein acetylation
H1990414biological_processreplication-born double-strand break repair via sister chromatid exchange
A0034990cellular_componentnuclear mitotic cohesin complex
A0003680molecular_functionAT DNA binding
A0005524molecular_functionATP binding
A0016887molecular_functionATPase activity
A0000217molecular_functionDNA secondary structure binding
A0003690molecular_functiondouble-stranded DNA binding
A0042802molecular_functionidentical protein binding
A0051301biological_processcell division
A0006302biological_processdouble-strand break repair
A0007064biological_processmitotic sister chromatid cohesion
A0000070biological_processmitotic sister chromatid segregation
B0034990cellular_componentnuclear mitotic cohesin complex
B0003680molecular_functionAT DNA binding
B0005524molecular_functionATP binding
B0016887molecular_functionATPase activity
B0000217molecular_functionDNA secondary structure binding
B0003690molecular_functiondouble-stranded DNA binding
B0042802molecular_functionidentical protein binding
B0051301biological_processcell division
B0006302biological_processdouble-strand break repair
B0007064biological_processmitotic sister chromatid cohesion
B0000070biological_processmitotic sister chromatid segregation
C0034990cellular_componentnuclear mitotic cohesin complex
C0003680molecular_functionAT DNA binding
C0005524molecular_functionATP binding
C0016887molecular_functionATPase activity
C0000217molecular_functionDNA secondary structure binding
C0003690molecular_functiondouble-stranded DNA binding
C0042802molecular_functionidentical protein binding
C0051301biological_processcell division
C0006302biological_processdouble-strand break repair
C0007064biological_processmitotic sister chromatid cohesion
C0000070biological_processmitotic sister chromatid segregation
D0034990cellular_componentnuclear mitotic cohesin complex
D0003680molecular_functionAT DNA binding
D0005524molecular_functionATP binding
D0016887molecular_functionATPase activity
D0000217molecular_functionDNA secondary structure binding
D0003690molecular_functiondouble-stranded DNA binding
D0042802molecular_functionidentical protein binding
D0051301biological_processcell division
D0006302biological_processdouble-strand break repair
D0007064biological_processmitotic sister chromatid cohesion
D0000070biological_processmitotic sister chromatid segregation
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC13BINDING SITE FOR RESIDUE MG A 2001
ChainResidue
ASER40
AGLN151
AAGS

AC23BINDING SITE FOR RESIDUE MG B 2001
ChainResidue
BSER40
BGLN151
BAGS

AC33BINDING SITE FOR RESIDUE MG C 2001
ChainResidue
CSER40
CGLN151
CAGS

AC43BINDING SITE FOR RESIDUE MG D 2001
ChainResidue
DSER40
DGLN151
DAGS

AC521BINDING SITE FOR RESIDUE AGS A 2224
ChainResidue
ALYS13
AASN35
AGLY36
ASER37
AGLY38
ALYS39
ASER40
AASN41
AASP64
AILE66
AARG68
AGLN151
AGLU363
AMG
BLYS326
BPHE328
BTYR333
BSER335
BGLY336
BGLY337
BGLU338

AC622BINDING SITE FOR RESIDUE AGS B 2224
ChainResidue
ALYS326
ATYR333
ASER335
AGLY336
AGLY337
AGLU338
BLYS13
BSER14
BASN35
BGLY36
BSER37
BGLY38
BLYS39
BSER40
BASN41
BASP64
BLEU65
BILE66
BARG68
BGLN151
BGLU363
BMG

AC723BINDING SITE FOR RESIDUE AGS C 2224
ChainResidue
CLYS13
CSER14
CPRO34
CASN35
CGLY36
CSER37
CGLY38
CLYS39
CSER40
CASN41
CASP64
CLEU65
CARG68
CGLN151
CGLU363
CMG
DLYS326
DPHE328
DTYR333
DSER335
DGLY336
DGLY337
DGLU338

AC821BINDING SITE FOR RESIDUE AGS D 2224
ChainResidue
CLYS326
CPHE328
CTYR333
CSER335
CGLY336
CGLY337
CGLU338
DLYS13
DSER14
DASN35
DGLY36
DSER37
DGLY38
DLYS39
DSER40
DASN41
DASP64
DARG68
DGLN151
DGLU363
DMG

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

site_idNumber of ResiduesDetails
AGS_1w1w_A_222430PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER binding site
ChainResidueligand
ALYS13-SER14AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
APRO34-MET42AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
AASP64-ARG68AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
AGLN151AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
AGLU1158AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ALEU1190AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
AARG1206AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
BPRO1118AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
BLYS1121AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
BPHE1123AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
BTYR1128-GLU1133AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
BALA1162AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

AGS_1w1w_B_222428PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER binding site
ChainResidueligand
ALYS1121AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
APHE1123AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATYR1128AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ASER1130-GLU1133AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
AALA1162AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
BLYS13-SER14AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
BPRO34-MET42AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
BASP64-ARG68AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
BGLN151AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
BGLU1158AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
BLEU1190AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
BARG1206AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

AGS_1w1w_C_222430PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER binding site
ChainResidueligand
CLYS13-SER14AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
CPRO34-MET42AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
CASP64-ARG68AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
CGLN151AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
CGLU1158AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
CLEU1190AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
CARG1206AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
DPRO1118AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
DLYS1121AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
DPHE1123AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
DTYR1128-GLU1133AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
DALA1162AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

AGS_1w1w_D_222429PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER binding site
ChainResidueligand
CLYS1121AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
CPHE1123AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
CTYR1128-GLU1133AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
CALA1162AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
DLYS13-SER14AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
DPRO34-MET42AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
DASP64-ARG68AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
DGLN151AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
DGLU1158AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
DLEU1190AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
DARG1206AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11ATP (Potential).
ChainResidueDetails
ANA*

SWS_FT_FI21ATP (Potential).
ChainResidueDetails
BNA*

SWS_FT_FI31ATP (Potential).
ChainResidueDetails
CNA*

SWS_FT_FI41ATP (Potential).
ChainResidueDetails
DNA*

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb1w1w.ent.gz (263.18 KB)
Display
all (no-compress)pdb1w1w.ent (1.09 MB)
header onlypdb1w1w.ent.gz (13.68 KB)
Display
PDBx/mmCIF1w1w.cif.gz (324.64 KB)
PDBMLall1w1w.xml.gz (499.07 KB)
Display
no-atom1w1w-noatom.xml.gz (68.65 KB)
Display
ext-atom1w1w-extatom.xml.gz (292.67 KB)
Display
PDBMLplusall1w1w-plus.xml.gz (502.9 KB)
Display
no-atom1w1w-plus-noatom.xml.gz (72.48 KB)
Display
add only1w1w-add.xml.gz (3.83 KB)
Display
RDF1w1w.rdf.gz (143.29 KB)
Display
Structure factorsr1w1wsf.ent.gz (454.13 KB)
Biological unit (PDB format)1w1w.pdb1.gz (69.53 KB) (B,F)
*software defined assembly, 2 molecule(s) (dimeric)
Display
1w1w.pdb2.gz (60.65 KB) (A,E)
*software defined assembly, 2 molecule(s) (dimeric)
Display
1w1w.pdb3.gz (69.81 KB) (D,H)
*software defined assembly, 2 molecule(s) (dimeric)
Display
1w1w.pdb4.gz (69.22 KB) (C,G)
*software defined assembly, 2 molecule(s) (dimeric)
Display
1w1w.pdb5.gz (124.47 KB) (A,B,E,F)
*author defined assembly, 4 molecule(s) (tetrameric)
Display
1w1w.pdb6.gz (133.55 KB) (C,D,G,H)
*author defined assembly, 4 molecule(s) (tetrameric)
Display
Validation reportsPDF1w1w​_validation.pdf.gz (353.38 KB)
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PDF-full1w1w​_full​_validation.pdf.gz (427.65 KB)
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XML1w1w​_validation.xml.gz (64.91 KB)
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PNG1w1w​_multipercentile​_validation.png.gz (149.88 KB)
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SVG1w1w​_multipercentile​_validation.svg.gz (944 B)
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Sequence (fasta)1w1w​_seq.txt
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