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- PDB-5hdt: Human cohesin regulator Pds5B bound to a Wapl peptide -

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Basic information

Entry
Database: PDB / ID: 5hdt
TitleHuman cohesin regulator Pds5B bound to a Wapl peptide
Components
  • Sister chromatid cohesion protein PDS5 homolog B
  • Wings apart-like protein homolog
KeywordsCELL CYCLE / cohesin regulator / Pds5B / Wapl / IP6
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 / mitotic sister chromatid cohesion / intercellular bridge / negative regulation of DNA replication / mitotic sister chromatid segregation / chromosome, centromeric region ...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 / mitotic sister chromatid cohesion / intercellular bridge / negative regulation of DNA replication / mitotic sister chromatid segregation / chromosome, centromeric region / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / mitotic spindle / Separation of Sister Chromatids / chromosome / regulation of cell population proliferation / cell population proliferation / negative regulation of cell population proliferation / cell division / intracellular membrane-bounded organelle / chromatin / DNA binding / 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. / Sister chromatid cohesion protein Pds5 / Sister chromatid cohesion protein PDS5 protein / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Wings apart-like protein homolog / Sister chromatid cohesion protein PDS5 homolog B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.711 Å
AuthorsOuyang, Z. / Tomchick, D.R. / Yu, H.
CitationJournal: To Be Published
Title: Structure of the human cohesin regulator Pds5 in complex with Wapl motif
Authors: Ouyang, Z. / Tomchick, D.R. / Yu, H.
History
DepositionJan 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 14, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sister chromatid cohesion protein PDS5 homolog B
B: Sister chromatid cohesion protein PDS5 homolog B
E: Wings apart-like protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,3825
Polymers262,0623
Non-polymers1,3202
Water00
1
A: Sister chromatid cohesion protein PDS5 homolog B
E: Wings apart-like protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,5333
Polymers132,8732
Non-polymers6601
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-10 kcal/mol
Surface area49950 Å2
MethodPISA
2
B: Sister chromatid cohesion protein PDS5 homolog B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8502
Polymers129,1901
Non-polymers6601
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-8 kcal/mol
Surface area49790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.760, 162.368, 173.061
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: Protein Sister chromatid cohesion protein PDS5 homolog B / Androgen-induced proliferation inhibitor / Androgen-induced prostate proliferative shutoff- ...Androgen-induced proliferation inhibitor / Androgen-induced prostate proliferative shutoff-associated protein AS3


Mass: 129189.531 Da / Num. of mol.: 2 / Fragment: UNP residues 21-1120 / Mutation: Y97H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDS5B, APRIN, AS3, KIAA0979 / Plasmid: pFastbacHT / Cell (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q9NTI5
#2: Protein/peptide Wings apart-like protein homolog / Friend of EBNA2 protein / WAPL cohesin release factor


Mass: 3683.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q7Z5K2
#3: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
Has protein modificationY
Sequence detailsY97H was not engineered on-purpose.

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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: 3.36 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Sodium Citrate and 20% PEG3350 (vol/vol) without buffer or with buffer 0.1 M Bis-Tris propane pH6.5, pH 7.5 or pH 8.5
PH range: 6.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2014
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→40.6 Å / Num. obs: 92470 / % possible obs: 99.9 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 18.4
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.711→40.6 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2533 1991 2.45 %
Rwork0.2161 --
obs0.217 81101 87.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.711→40.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17432 0 72 0 17504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317837
X-RAY DIFFRACTIONf_angle_d0.62124108
X-RAY DIFFRACTIONf_dihedral_angle_d11.9826804
X-RAY DIFFRACTIONf_chiral_restr0.0632779
X-RAY DIFFRACTIONf_plane_restr0.0033029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.711-2.77850.4327610.32862181X-RAY DIFFRACTION34
2.7785-2.85360.3543860.32083466X-RAY DIFFRACTION54
2.8536-2.93750.30861050.29274283X-RAY DIFFRACTION67
2.9375-3.03230.32131310.27684984X-RAY DIFFRACTION78
3.0323-3.14060.2811410.27585757X-RAY DIFFRACTION90
3.1406-3.26630.34011600.26996349X-RAY DIFFRACTION99
3.2663-3.41490.30191580.25826407X-RAY DIFFRACTION100
3.4149-3.59490.26581710.23146425X-RAY DIFFRACTION100
3.5949-3.81990.22451620.20866448X-RAY DIFFRACTION100
3.8199-4.11460.2481610.20036455X-RAY DIFFRACTION100
4.1146-4.52820.21381600.1746484X-RAY DIFFRACTION100
4.5282-5.18230.21741600.176525X-RAY DIFFRACTION100
5.1823-6.52480.2361680.22176558X-RAY DIFFRACTION100
6.5248-40.59650.2081670.17576788X-RAY DIFFRACTION100
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)
10.058-0.0211-0.09250.03230.00220.0843-0.05020.0255-0.125-0.161-0.03070.0233-0.03540.1113-0.16090.0929-0.22160.1620.09080.1446-0.129111.2023115.1401155.0036
20.01450.0006-0.00280.00420.00440.0079-0.00180.01690.0069-0.0157-0.0095-0.0083-0.00310.0044-0.02090.02420.01950.03010.0980.04860.093873.806194.907195.2437
30.0025-0.00180.01220.004800.04690.0544-0.0356-0.00690.0769-0.0474-0.0760.05670.00020.03210.1219-0.06170.02780.06220.11420.183391.275669.7733218.2946
40.01990.01220.01270.01570.00780.01190.0072-0.07290.03090.0268-0.06440.014-0.0375-0.0397-0.00830.16510.0155-0.10460.1387-0.0410.298592.7068101.2367234.4729
50.04140.0073-0.00250.04070.01850.0182-0.0048-0.09980.05890.09650.0247-0.01480.00660.07850.03090.2435-0.0925-0.09930.32880.0177-0.0349116.5949129.8651227.2702
60.01980.004-0.00910.0147-0.00730.01540.036-0.02730.0170.01820.01170.00090.0056-0.02730.08130.1312-0.1273-0.14110.1140.06280.218792.1829160.402179.0008
70.0669-0.0646-0.0390.06760.03730.07690.05290.06250.0414-0.0384-0.06520.0566-0.0667-0.06180.00570.07950.0429-0.07270.03390.02520.474895.803163.5957141.7898
80.00050.0001-0.00030.00120.00170.00280.00040.00090.00020.0002-0.0010.0001-0.0001000.7101-0.00550.01120.7104-0.010.713130.5115123.2882129.8085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 485 )
2X-RAY DIFFRACTION2chain 'A' and (resid 486 through 608 )
3X-RAY DIFFRACTION3chain 'A' and (resid 609 through 859 )
4X-RAY DIFFRACTION4chain 'A' and (resid 860 through 1116 )
5X-RAY DIFFRACTION5chain 'B' and (resid 20 through 363 )
6X-RAY DIFFRACTION6chain 'B' and (resid 364 through 608 )
7X-RAY DIFFRACTION7chain 'B' and (resid 609 through 1120 )
8X-RAY DIFFRACTION8chain 'E' and (resid 7 through 11 )

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