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- PDB-4k6j: Human cohesin inhibitor WapL -

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Basic information

Entry
Database: PDB / ID: 4k6j
TitleHuman cohesin inhibitor WapL
ComponentsWings apart-like protein homolog
KeywordsCELL CYCLE / heat repeats / cohesin regulator / Cell Adhesion Inhibitor / nuclear protein / protein-binding
Function / homology
Function and homology information


negative regulation of chromatin binding / ATP-dependent protein-DNA unloader activity / negative regulation of sister chromatid cohesion / Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / negative regulation of DNA replication / mitotic sister chromatid segregation / chromosome, centromeric region / intercellular bridge / protein localization to chromatin ...negative regulation of chromatin binding / ATP-dependent protein-DNA unloader activity / negative regulation of sister chromatid cohesion / Cohesin Loading onto Chromatin / Establishment of Sister Chromatid Cohesion / negative regulation of DNA replication / mitotic sister chromatid segregation / chromosome, centromeric region / intercellular bridge / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Separation of Sister Chromatids / mitotic spindle / chromosome / cell division / intracellular membrane-bounded organelle / chromatin / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
WAPL domain / Wings apart-like protein, C-terminal / Wings apart-like protein / Wings apart-like protein regulation of heterochromatin / WAPL domain profile. / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Wings apart-like protein homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6205 Å
AuthorsTomchick, D.R. / Yu, H. / Ouyang, Z.
Citation
#1: Journal: Nat.Cell Biol. / Year: 2013
Title: Phosphorylation-enabled binding of SGO1-PP2A to cohesin protects sororin and centromeric cohesion during mitosis.
Authors: Liu, H. / Rankin, S. / Yu, H.
History
DepositionApr 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Wings apart-like protein homolog
B: Wings apart-like protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,32217
Polymers127,9552
Non-polymers1,36715
Water1,910106
1
A: Wings apart-like protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,76810
Polymers63,9781
Non-polymers7919
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Wings apart-like protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5547
Polymers63,9781
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.540, 107.540, 300.608
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsAuthors indicate that size exclusion chromatography, multi-angle light scattering, analytical ultracentrifugation indicate that WapL is monomeric in solution.

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Components

#1: Protein Wings apart-like protein homolog / Friend of EBNA2 protein


Mass: 63977.539 Da / Num. of mol.: 2 / Fragment: Wapl C-terminal domain (UNP Residues 631-1190)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WAPAL, FOE, KIAA0261, WAPL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7Z5K2
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.4 Å3/Da / Density % sol: 63.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 1.4 M ammonium sulfate, 0.1 M HEPES pH 7.1, 10% glycerol, vapor diffusion, sitting drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.979183
SYNCHROTRONAPS 19-ID20.97921
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 315r1CCDMar 15, 2012monochromator
ADSC QUANTUM 315r2CCDMar 15, 2012monochromator
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHx-ray1
2SAGITALLY FOCUSED Si(111)SADx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791831
20.979211
ReflectionResolution: 2.62→50 Å / Num. all: 53851 / Num. obs: 53851 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.056 / Χ2: 0.969 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.62-2.674.80.55826080.9561,299.8
2.67-2.714.80.49526430.9491,2100
2.71-2.774.90.39126600.931,2100
2.77-2.824.90.36326590.9451,2100
2.82-2.884.90.29926360.971,2100
2.88-2.954.90.22926610.9471,2100
2.95-3.024.90.19326500.9681,299.9
3.02-3.114.90.1626850.951,2100
3.11-3.24.90.13526610.9631,2100
3.2-3.34.90.10426830.9371,2100
3.3-3.424.90.08326550.9651,299.9
3.42-3.564.90.06227020.9521,299.9
3.56-3.724.90.04726970.8381,299.7
3.72-3.914.90.03926750.8371,299.7
3.91-4.164.90.03327100.7931,299.6
4.16-4.484.80.03427070.9851,299.4
4.48-4.934.80.03727311.3571,299.5
4.93-5.644.80.04427331.5321,299.1
5.64-7.114.70.03527781.0861,298.7
7.11-504.40.01729170.5211,297

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6205→29.68 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / σ(F): 1.35 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 2584 5.05 %random
Rwork0.1843 ---
all0.1869 51154 --
obs0.1869 51154 94.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 183.77 Å2 / Biso mean: 52.1503 Å2 / Biso min: 7.2 Å2
Refine analyzeLuzzati sigma a obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.6205→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7648 0 73 106 7827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027813
X-RAY DIFFRACTIONf_angle_d0.63710546
X-RAY DIFFRACTIONf_chiral_restr0.0391223
X-RAY DIFFRACTIONf_plane_restr0.0021345
X-RAY DIFFRACTIONf_dihedral_angle_d14.4342921
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6205-2.67080.3117870.21871590167758
2.6708-2.72530.2647990.21692076217574
2.7253-2.78450.26531220.2152421254387
2.7845-2.84920.32791450.21362671281695
2.8492-2.92040.27231580.20922764292299
2.9204-2.99930.28461490.206727702919100
2.9993-3.08750.29211600.214628022962100
3.0875-3.1870.28461530.20928142967100
3.187-3.30080.27721650.207127952960100
3.3008-3.43280.23811360.188128342970100
3.4328-3.58880.22111390.178128512990100
3.5888-3.77760.2131570.160728032960100
3.7776-4.01380.20961480.153628482996100
4.0138-4.32280.1841450.150828583003100
4.3228-4.75620.18991610.14742842300399
4.7562-5.44080.20311460.17192889303599
5.4408-6.8410.28421760.24322882305899
6.841-29.68240.21381380.18153060319897
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.00280.00070.00150.00020.00060.0009-0.00550.0109-0.01060.00110.0149-0.01-0.0068-0.004500.13740.003-0.01630.183-0.07580.1969113.977711.663163.0865
20.01660.0017-0.00350.0209-0.02090.0230.04310.00520.0267-0.05790.0784-0.03720.01080.0330.0260.1268-0.0196-0.04220.2167-0.12830.1959102.4555-2.363346.4864
30.0150.009-0.02320.0055-0.010.03070.02510.0311-0.00580.02020.03-0.0420.14720.03770.00570.14720.0426-0.05360.1046-0.03760.192391.9627-8.075757.9717
40.00860.0174-0.01520.0514-0.04350.03520.0718-0.0787-0.01030.1253-0.0286-0.03840.1592-0.03510.01980.2656-0.1101-0.0769-0.05810.02150.171282.6632-10.215584.3601
50.00530.0005-0.00470.0020.00320.0101-0.01160.00810.00780.04910.0664-0.00870.0137-0.0656-00.25430.08480.07560.38550.02650.333855.511525.200986.6194
60.0368-0.00870.03530.01480.00320.05410.0172-0.04530.05220.03050.02710.05440.0057-0.06180.0520.12010.05680.0710.2960.0710.241954.879420.258967.4818
70.0268-0.00920.03320.0359-0.01820.06120.0009-0.0124-0.0144-0.00650.0750.04950.0061-0.04450.10170.03720.1106-0.00460.17620.13670.064770.489823.975850.0012
80.0075-0.0061-0.00320.01280.00050.0153-0.07860.01940.01530.03950.0417-0.0192-0.07990.0307-00.17810.0059-0.01580.1770.0320.12385.696240.398549.4804
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -7 through 651 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 652 through 737 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 738 through 840 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 841 through 1190 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid -7 through 670 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 671 through 840 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 841 through 973 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 974 through 1190 )B0

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