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- PDB-6n31: WD repeats of human WDR12 -

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Basic information

Entry
Database: PDB / ID: 6n31
TitleWD repeats of human WDR12
ComponentsRibosome biogenesis protein WDR12
KeywordsPROTEIN BINDING / WD repeat / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


PeBoW complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, large subunit precursor / Major pathway of rRNA processing in the nucleolus and cytosol / ribonucleoprotein complex binding / Notch signaling pathway / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / regulation of cell cycle / nucleolus / nucleoplasm
Similarity search - Function
WD repeat WDR12/Ytm1 / NLE / NLE (NUC135) domain / 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. / WD domain, G-beta repeat / WD40 repeats ...WD repeat WDR12/Ytm1 / NLE / NLE (NUC135) domain / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Ribosome biogenesis protein WDR12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHalabelian, L. / Zeng, H. / Tempel, W. / Li, Y. / Seitova, A. / Hutchinson, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: WD repeats of human WDR12
Authors: Halabelian, L. / Zeng, H. / Tempel, W. / Li, Y. / Seitova, A. / Hutchinson, A. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H.
History
DepositionNov 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome biogenesis protein WDR12
B: Ribosome biogenesis protein WDR12


Theoretical massNumber of molelcules
Total (without water)78,60438
Polymers78,6042
Non-polymers036
Water00
1
A: Ribosome biogenesis protein WDR12


Theoretical massNumber of molelcules
Total (without water)39,30215
Polymers39,3021
Non-polymers014
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribosome biogenesis protein WDR12


Theoretical massNumber of molelcules
Total (without water)39,30223
Polymers39,3021
Non-polymers022
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.740, 87.050, 155.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribosome biogenesis protein WDR12 / WD repeat-containing protein 12


Mass: 39302.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR12 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9GZL7
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 36 / 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: 2.28 Å3/Da / Density % sol: 45.96 % / Mosaicity: 0.11 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG 3350, 0.2M magnesium chloride, 0.1M Hepes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→76 Å / Num. obs: 21949 / % possible obs: 96.7 % / Redundancy: 3 % / Biso Wilson estimate: 64.83 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.074 / Rrim(I) all: 0.134 / Net I/σ(I): 7.3 / Num. measured all: 65007 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.712.90.837721262577210.6540.571.0121.295.7
9-763.10.038165053116500.9970.0250.04622.490

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ow8, side chains modeled with FFAS03/SCWRL

3ow8


Resolution: 2.6→76 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.915 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.681 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.672 / SU Rfree Blow DPI: 0.28 / SU Rfree Cruickshank DPI: 0.285
Details: Structure factor amplitudes were derived from the first 400 0.2 degree diffraction images of the data set.
RfactorNum. reflection% reflection
Rfree0.233 1046 4.78 %
Rwork0.203 --
obs0.205 21880 95.9 %
Displacement parametersBiso max: 128.49 Å2 / Biso mean: 49.56 Å2 / Biso min: 13.57 Å2
Baniso -1Baniso -2Baniso -3
1--3.0593 Å20 Å20 Å2
2---2.6114 Å20 Å2
3---5.6706 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: final / Resolution: 2.6→76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4677 0 36 0 4713
Biso mean--35.2 --
Num. residues----620
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1585SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes79HARMONIC2
X-RAY DIFFRACTIONt_gen_planes717HARMONIC5
X-RAY DIFFRACTIONt_it4826HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion660SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5338SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4826HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6592HARMONIC21.3
X-RAY DIFFRACTIONt_omega_torsion3.59
X-RAY DIFFRACTIONt_other_torsion18.53
LS refinement shellResolution: 2.6→2.73 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.288 114 3.98 %
Rwork0.221 2748 -
all-2862 -
obs--95.98 %
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)
12.3296-1.03570.44281.2221-0.40541.8662-0.2195-0.39010.13510.3110.1475-0.0602-0.0699-0.19010.072-0.10390.0245-0.02-0.07650.0019-0.1370.0389-27.9797-25.3058
21.3060.52470.35361.46470.4641.7178-0.05950.032-0.0169-0.3460.07970.04320.0034-0.0678-0.0202-0.04620.02350.0044-0.11190.0182-0.1089-26.3564-24.1473-58.9862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|91 - A|414 }A91 - 414
2X-RAY DIFFRACTION2{ B|91 - B|415 }B91 - 415

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