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- PDB-3ow8: Crystal Structure of the WD repeat-containing protein 61 -

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Basic information

Entry
Database: PDB / ID: 3ow8
TitleCrystal Structure of the WD repeat-containing protein 61
ComponentsWD repeat-containing protein 61
KeywordsTRANSCRIPTION / WD repeat / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Ski complex / mRNA decay by 3' to 5' exoribonuclease / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / negative regulation of myeloid cell differentiation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / rescue of stalled ribosome / transcription elongation by RNA polymerase II ...Ski complex / mRNA decay by 3' to 5' exoribonuclease / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / negative regulation of myeloid cell differentiation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / rescue of stalled ribosome / transcription elongation by RNA polymerase II / euchromatin / Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
: / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. ...: / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Superkiller complex protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsTempel, W. / Li, Z. / Chao, X. / Lam, R. / Wernimont, A.K. / He, H. / Seitova, A. / Pan, P.W. / Li, Y. / Bountra, C. ...Tempel, W. / Li, Z. / Chao, X. / Lam, R. / Wernimont, A.K. / He, H. / Seitova, A. / Pan, P.W. / Li, Y. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Protein Cell / Year: 2011
Title: Structure and function of WD40 domain proteins.
Authors: Xu, C. / Min, J.
History
DepositionSep 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WD repeat-containing protein 61
B: WD repeat-containing protein 61
C: WD repeat-containing protein 61
D: WD repeat-containing protein 61


Theoretical massNumber of molelcules
Total (without water)142,51839
Polymers142,5184
Non-polymers035
Water00
1
A: WD repeat-containing protein 61


Theoretical massNumber of molelcules
Total (without water)35,6307
Polymers35,6301
Non-polymers06
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: WD repeat-containing protein 61


Theoretical massNumber of molelcules
Total (without water)35,6307
Polymers35,6301
Non-polymers06
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: WD repeat-containing protein 61


Theoretical massNumber of molelcules
Total (without water)35,63014
Polymers35,6301
Non-polymers013
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: WD repeat-containing protein 61


Theoretical massNumber of molelcules
Total (without water)35,63011
Polymers35,6301
Non-polymers010
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.544, 72.922, 81.514
Angle α, β, γ (deg.)114.340, 96.440, 90.120
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13A
23C
14A
24C
15B
25C
16B
26C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111TYRTYRLEULEU2AA5 - 6021 - 76
211TYRTYRLEULEU2BB5 - 6021 - 76
121GLNGLNLEULEU4AA64 - 22880 - 244
221GLNGLNLEULEU4BB64 - 22880 - 244
131ALAALAPROPRO4AA232 - 304248 - 320
231ALAALAPROPRO4BB232 - 304248 - 320
112TYRTYRPROPRO2CC5 - 30421 - 320
212TYRTYRPROPRO2DD5 - 30421 - 320
113SERSERHISHIS2AA229 - 231245 - 247
213SERSERHISHIS2CC229 - 231245 - 247
114GLUGLUHISHIS2AA61 - 6377 - 79
214GLUGLUHISHIS2CC61 - 6377 - 79
115SERSERHISHIS3BB229 - 231245 - 247
215SERSERHISHIS3CC229 - 231245 - 247
116GLUGLUHISHIS3BB61 - 6377 - 79
216GLUGLUHISHIS3CC61 - 6377 - 79

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
WD repeat-containing protein 61 / Meiotic recombination REC14 protein homolog


Mass: 35629.582 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR61 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q9GZS3
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 35 / Source method: obtained synthetically

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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: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Mix 0.5uL precipitant (6% PEG20000, 8% PEG-MME550, 0.2M calcium acetate), 0.5uL protein stock solution (11 mg/mL protein), 0.2 uL additive (5% w/v polyvinylpyrrolidine K15), vapor diffusion, ...Details: Mix 0.5uL precipitant (6% PEG20000, 8% PEG-MME550, 0.2M calcium acetate), 0.5uL protein stock solution (11 mg/mL protein), 0.2 uL additive (5% w/v polyvinylpyrrolidine K15), vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 58481 / % possible obs: 97.8 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.106 / Χ2: 1.868 / Net I/σ(I): 9.89
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.3-2.341.80.8651.0528981.91596
2.34-2.381.80.78128821.78396.8
2.38-2.431.80.73529051.81296.9
2.43-2.481.90.63528941.68897.3
2.48-2.531.90.58229131.90297.4
2.53-2.591.90.56429311.82697.5
2.59-2.661.90.44429021.80997.5
2.66-2.731.90.37429181.90597.6
2.73-2.811.90.32429701.89998.1
2.81-2.91.90.26528861.93998
2.9-31.90.19829231.78498.2
3-3.121.90.17429631.9398.2
3.12-3.261.90.13229291.8798.2
3.26-3.441.90.10429181.89398.2
3.44-3.651.90.07929501.8998.5
3.65-3.931.90.06829361.94398.3
3.93-4.331.90.05529521.94398.5
4.33-4.951.90.04229471.81898.5
4.95-6.241.90.04829371.72798.9
6.24-4020.04629272.05797.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3frx

3frx


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.257 / WRfactor Rwork: 0.226 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.543 / SU ML: 0.245
Cross valid method: THROUGHOUT. Change of flag assignment was followed by slow-cool simulated annealing (from temperature = 5000.0, phenix).
σ(F): 0 / ESU R: 0.369 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED. Programs chainsaw, resolve, buccaneer, phenix, autobuster, coot and the molprobity server were also used during refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2766 2000 3.434 %phenix.reflection_file_converter --use-lattice-symmetry-in-r-free-flag-generation
Rwork0.244 ---
obs0.245 58241 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso max: 79.65 Å2 / Biso mean: 29.377 Å2 / Biso min: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.228 Å2-0.256 Å2-0.235 Å2
2---0.925 Å20.491 Å2
3---3.505 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8828 0 35 0 8863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0219056
X-RAY DIFFRACTIONr_bond_other_d0.0010.025573
X-RAY DIFFRACTIONr_angle_refined_deg1.11.91912391
X-RAY DIFFRACTIONr_angle_other_deg0.812313657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1851179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4324.768367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38151266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0221515
X-RAY DIFFRACTIONr_chiral_restr0.0660.21413
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210364
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021843
X-RAY DIFFRACTIONr_mcbond_it0.2491.55852
X-RAY DIFFRACTIONr_mcbond_other0.0661.52433
X-RAY DIFFRACTIONr_mcangle_it0.45629326
X-RAY DIFFRACTIONr_scbond_it0.7933204
X-RAY DIFFRACTIONr_scangle_it1.2134.53065
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A285TIGHT POSITIONAL0.070.05
1A3128MEDIUM POSITIONAL0.110.5
1A285TIGHT THERMAL0.190.5
1A3128MEDIUM THERMAL0.192
2C1766TIGHT POSITIONAL0.020.05
2C1875MEDIUM POSITIONAL0.020.5
2C1766TIGHT THERMAL0.040.5
2C1875MEDIUM THERMAL0.042
3A17TIGHT POSITIONAL0.040.05
3A13MEDIUM POSITIONAL0.030.5
3A17TIGHT THERMAL0.040.5
3A13MEDIUM THERMAL0.052
4A17TIGHT POSITIONAL0.020.05
4A21MEDIUM POSITIONAL0.030.5
4A17TIGHT THERMAL0.050.5
4A21MEDIUM THERMAL0.052
5B17TIGHT POSITIONAL0.030.05
5B13LOOSE POSITIONAL0.035
5B17TIGHT THERMAL0.050.5
5B13LOOSE THERMAL0.0910
6B17TIGHT POSITIONAL0.010.05
6B21LOOSE POSITIONAL0.045
6B17TIGHT THERMAL0.060.5
6B21LOOSE THERMAL0.0510
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.3590.4021480.37840254173
2.359-2.4240.4221470.37139874134
2.424-2.4930.341360.35339524088
2.493-2.570.4051320.33637563888
2.57-2.6530.3531330.31536893822
2.653-2.7460.311230.2935533676
2.746-2.8480.3011190.26334503569
2.848-2.9630.341180.25333573475
2.963-3.0940.2831120.23732083320
3.094-3.2430.2791170.22930643181
3.243-3.4160.249970.22729033000
3.416-3.6210.243960.21927972893
3.621-3.8670.249930.22125782671
3.867-4.1710.217880.224212509
4.171-4.560.201800.17722472327
4.56-5.0840.2770.1820192096
5.084-5.8420.252610.22918201881
5.842-7.0880.334560.25415261582
7.088-9.7560.253430.26211971240
9.756-300.289240.26692716
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)
12.51280.48180.10222.6918-0.00182.14410.0844-0.23370.31740.3174-0.12910.308-0.214-0.07350.04470.1398-0.00360.02570.0281-0.04740.1311.770820.219951.7681
22.2668-0.0707-0.03182.37430.27221.88230.0580.1592-0.2039-0.1631-0.03130.07320.1909-0.0664-0.02680.1230.0149-0.04130.0236-0.00460.058-20.689726.675719.7435
32.59360.28290.30551.78980.4512.0754-0.02490.23570.2493-0.2767-0.04050.0661-0.1602-0.00540.06540.05180.0081-0.01550.0250.02390.0376-19.353-12.528619.7952
42.3019-0.09030.12642.14880.30481.95690.0468-0.2058-0.11230.2779-0.06320.06020.1563-0.11140.01640.0486-0.01730.00420.02550.00690.007713.0173-13.313851.8319
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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