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- PDB-6cvz: Crystal structure of the WD40-repeat of RFWD3 -

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Basic information

Entry
Database: PDB / ID: 6cvz
TitleCrystal structure of the WD40-repeat of RFWD3
ComponentsE3 ubiquitin-protein ligase RFWD3
KeywordsTRANSFERASE / WD40-repeat / RFWD3 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of DNA damage checkpoint / response to ionizing radiation / replication fork processing / site of DNA damage / interstrand cross-link repair / mitotic G1 DNA damage checkpoint signaling / MDM2/MDM4 family protein binding / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / PML body ...regulation of DNA damage checkpoint / response to ionizing radiation / replication fork processing / site of DNA damage / interstrand cross-link repair / mitotic G1 DNA damage checkpoint signaling / MDM2/MDM4 family protein binding / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / PML body / p53 binding / ubiquitin protein ligase activity / protein ubiquitination / DNA damage response / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase RFWD3 / Ring finger domain / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RFWD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsDONG, A. / LOPPNAU, P. / SEITOVA, A. / HUTCHINSON, A. / TEMPEL, W. / WEI, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. ...DONG, A. / LOPPNAU, P. / SEITOVA, A. / HUTCHINSON, A. / TEMPEL, W. / WEI, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / TONG, Y. / Structural Genomics Consortium (SGC)
CitationJournal: Proteins / Year: 2019
Title: Target highlights in CASP13: Experimental target structures through the eyes of their authors.
Authors: Lepore, R. / Kryshtafovych, A. / Alahuhta, M. / Veraszto, H.A. / Bomble, Y.J. / Bufton, J.C. / Bullock, A.N. / Caba, C. / Cao, H. / Davies, O.R. / Desfosses, A. / Dunne, M. / Fidelis, K. / ...Authors: Lepore, R. / Kryshtafovych, A. / Alahuhta, M. / Veraszto, H.A. / Bomble, Y.J. / Bufton, J.C. / Bullock, A.N. / Caba, C. / Cao, H. / Davies, O.R. / Desfosses, A. / Dunne, M. / Fidelis, K. / Goulding, C.W. / Gurusaran, M. / Gutsche, I. / Harding, C.J. / Hartmann, M.D. / Hayes, C.S. / Joachimiak, A. / Leiman, P.G. / Loppnau, P. / Lovering, A.L. / Lunin, V.V. / Michalska, K. / Mir-Sanchis, I. / Mitra, A.K. / Moult, J. / Phillips Jr., G.N. / Pinkas, D.M. / Rice, P.A. / Tong, Y. / Topf, M. / Walton, J.D. / Schwede, T.
History
DepositionMar 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RFWD3
B: E3 ubiquitin-protein ligase RFWD3
C: E3 ubiquitin-protein ligase RFWD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4706
Polymers116,3973
Non-polymers733
Water5,134285
1
A: E3 ubiquitin-protein ligase RFWD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8232
Polymers38,7991
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase RFWD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8232
Polymers38,7991
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: E3 ubiquitin-protein ligase RFWD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8232
Polymers38,7991
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.991, 91.991, 110.738
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein E3 ubiquitin-protein ligase RFWD3 / RING finger and WD repeat domain-containing protein 3 / RING finger protein 201


Mass: 38798.969 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RFWD3, RNF201 / Plasmid: pFBOH-MHL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: Q6PCD5, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.08 % / Mosaicity: 0.36 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16% PEG 3500, 0.2 M Magnesium Chloride, 0.1 M Tris pH8.0

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Data collection

DiffractionMean temperature: 100 K
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: 1.8→30 Å / Num. obs: 96621 / % possible obs: 99.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.049 / Rrim(I) all: 0.099 / Χ2: 1.969 / Net I/σ(I): 7.4 / Num. measured all: 397184
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.834.10.68948840.7570.3860.7920.41699.9
1.83-1.8640.53947940.7950.3070.6220.44199.9
1.86-1.93.80.45548900.8430.2670.5290.46899.7
1.9-1.943.60.34147910.9020.2080.4010.52498.9
1.94-1.9840.31648750.9170.1790.3640.5499.7
1.98-2.034.40.28548440.9360.1540.3250.60899.9
2.03-2.084.50.25947990.9430.1390.2940.65999.9
2.08-2.134.50.22549310.9520.1210.2560.77199.8
2.13-2.24.40.19347920.9620.1050.220.88799.7
2.2-2.274.30.17248480.9670.0940.1971.04999.7
2.27-2.354.30.15748580.9670.0870.181.22899.6
2.35-2.444.20.14248320.9710.0790.1641.41199.5
2.44-2.554.10.13348750.970.0760.1541.67799.7
2.55-2.693.80.11847960.9770.070.1382.06999.3
2.69-2.863.70.10548230.9770.0630.1232.7799.2
2.86-3.084.40.09448680.9840.0510.1083.55499.6
3.08-3.394.30.08148180.9850.0450.0934.5599.5
3.39-3.884.10.07148110.9870.040.0825.298.6
3.88-4.883.80.06447450.9890.0380.0756.66697.8
4.88-3040.05647470.9760.0320.0654.50797.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished model

Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.723 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 962 1 %RANDOM
Rwork0.2143 ---
obs0.2146 95577 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.78 Å2 / Biso mean: 35.75 Å2 / Biso min: 10.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20.39 Å2-0 Å2
2--0.78 Å20 Å2
3----2.53 Å2
Refinement stepCycle: final / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7560 0 3 293 7856
Biso mean--39.21 37.47 -
Num. residues----1001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197923
X-RAY DIFFRACTIONr_bond_other_d0.0010.026935
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.94710838
X-RAY DIFFRACTIONr_angle_other_deg0.731316097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59851027
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97924.094320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.297151186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7321532
X-RAY DIFFRACTIONr_chiral_restr0.0780.21230
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219001
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021619
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 87 -
Rwork0.309 7138 -
all-7225 -
obs--99.86 %

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