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- PDB-5zc4: Crystal Structure of RNF13 RING domain -

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Basic information

Entry
Database: PDB / ID: 5zc4
TitleCrystal Structure of RNF13 RING domain
ComponentsE3 ubiquitin-protein ligase RNF13
KeywordsENDOCYTOSIS / Ubiquitin RING E3 ligase / PA-TM-RING protein / RNF13
Function / homology
Function and homology information


organelle localization / positive regulation of stress-activated protein kinase signaling cascade / JUN kinase binding / nuclear inner membrane / protein autoubiquitination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / late endosome membrane / ubiquitin-dependent protein catabolic process ...organelle localization / positive regulation of stress-activated protein kinase signaling cascade / JUN kinase binding / nuclear inner membrane / protein autoubiquitination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / late endosome membrane / ubiquitin-dependent protein catabolic process / endosome / lysosomal membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / endoplasmic reticulum / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
ZNRF4 /RNF13/RNF167, PA domain / Ring finger domain / PA domain superfamily / PA domain / PA domain / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.906 Å
AuthorsDatta, A.B. / Sarkar, S.
Funding support India, 1items
OrganizationGrant numberCountry
Wellcome Trust500241/Z/11/Z India
CitationJournal: To Be Published
Title: Crystal Structure of RNF13 RING domain
Authors: Sarkar, S. / Datta, A.B.
History
DepositionFeb 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: E3 ubiquitin-protein ligase RNF13
D: E3 ubiquitin-protein ligase RNF13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9436
Polymers17,6812
Non-polymers2624
Water1,40578
1
A: E3 ubiquitin-protein ligase RNF13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9713
Polymers8,8401
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20 Å2
ΔGint-3 kcal/mol
Surface area5030 Å2
MethodPISA
2
D: E3 ubiquitin-protein ligase RNF13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9713
Polymers8,8401
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.338, 90.338, 45.445
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-1142-

HOH

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Components

#1: Protein E3 ubiquitin-protein ligase RNF13 / RING finger protein 13 / RING-type E3 ubiquitin transferase RNF13


Mass: 8840.479 Da / Num. of mol.: 2 / Fragment: truncated RING domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF13, RZF / Plasmid: pETSUMO2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3)
References: UniProt: O43567, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100% Tacsimate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 18, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.906→45.17 Å / Num. obs: 16628 / % possible obs: 99.4 % / Redundancy: 8.8 % / Biso Wilson estimate: 36.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.018 / Net I/σ(I): 24.6
Reflection shellResolution: 1.906→1.95 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1071 / CC1/2: 0.793 / Rpim(I) all: 0.298 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
SHELXDphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.906→22.619 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1858 795 4.79 %Random
Rwork0.1662 ---
obs0.1671 16599 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.906→22.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1180 0 0 78 1258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151242
X-RAY DIFFRACTIONf_angle_d1.4311672
X-RAY DIFFRACTIONf_dihedral_angle_d14.098790
X-RAY DIFFRACTIONf_chiral_restr0.102181
X-RAY DIFFRACTIONf_plane_restr0.012213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9055-2.02480.26991430.23882569X-RAY DIFFRACTION99
2.0248-2.1810.20771170.20122652X-RAY DIFFRACTION100
2.181-2.40030.23791260.18232639X-RAY DIFFRACTION100
2.4003-2.74710.20251420.18372627X-RAY DIFFRACTION100
2.7471-3.45910.2091320.18272663X-RAY DIFFRACTION100
3.4591-22.62030.15461350.14192654X-RAY DIFFRACTION98
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)
17.51121.525-2.27466.60321.58691.3557-0.31670.40421.011-1.46030.0741-0.3024-0.23981.2299-0.0161.14340.4490.07671.44450.07520.612234.165936.7741-9.9287
29.73983.7399-3.86022.8194-4.48968.3718-0.51281.6911-1.9076-1.4531-0.3216-0.77022.1120.60660.57841.04090.34590.04020.8711-0.25580.836627.077624.8521-6.6127
35.926-3.29244.20634.0094-0.27414.9482-0.4755-0.7383-2.84030.6241-0.34972.14692.7372-0.91620.85960.9767-0.0680.11170.45760.01391.362617.107818.9918.1946
47.6362-0.3633-1.75349.59254.60832.83870.29860.4427-2.0127-0.3544-0.66631.35910.7944-0.42060.39450.49320.0888-0.10970.4553-0.12010.723818.381528.03215.2272
56.32010.4371-1.49596.62761.55684.62750.63171.0726-0.2893-1.1068-0.5397-0.22990.22960.3769-0.02940.54050.29960.02670.5493-0.01660.338829.078733.2286-0.0488
66.94911.0403-0.54782.0556-3.43839.12850.3201-0.0690.9974-0.05720.7534-0.3624-0.83380.0629-1.16570.4026-0.07640.02860.9276-0.05771.042741.990445.195416.1117
74.63596.1037-1.5419.8933-2.10145.7555-0.6148-1.3556-0.46710.35250.6306-1.29990.07320.7397-0.05360.38710.1784-0.07231.079-0.05640.793241.029433.62822.3279
80.2041-1.08350.19067.6351-2.69971.6908-0.0645-2.9781-2.82242.0490.62351.3791.6642-0.4079-0.55880.9623-0.0466-0.06561.15070.60091.120127.107221.411424.988
92.6677-2.23273.97568.1242-1.53588.50920.3976-1.9835-1.740.56320.20090.39841.5755-0.2724-0.57390.52650.11780.00390.79670.27440.63227.152428.245118.9469
109.1621.48772.06627.5087-2.1257.0958-0.1346-1.61731.09280.5721-0.0877-0.4244-0.3090.71860.19420.27840.1025-0.02350.8188-0.14580.531132.772739.992719.305
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 215:219 )A215 - 219
2X-RAY DIFFRACTION2( CHAIN A AND RESID 220:230 )A220 - 230
3X-RAY DIFFRACTION3( CHAIN A AND RESID 231:235 )A231 - 235
4X-RAY DIFFRACTION4( CHAIN A AND RESID 236:255 )A236 - 255
5X-RAY DIFFRACTION5( CHAIN A AND ( RESID 256:287 OR RESID 1001:1002 ) )A256 - 287
6X-RAY DIFFRACTION5( CHAIN A AND ( RESID 256:287 OR RESID 1001:1002 ) )A1001 - 1002
7X-RAY DIFFRACTION6( CHAIN D AND RESID 216:219 )D216 - 219
8X-RAY DIFFRACTION7( CHAIN D AND RESID 220:230 )D220 - 230
9X-RAY DIFFRACTION8( CHAIN D AND RESID 231:235 )D231 - 235
10X-RAY DIFFRACTION9( CHAIN D AND RESID 236:255 )D236 - 255
11X-RAY DIFFRACTION10( CHAIN D AND ( RESID 256:287 OR RESID 1001:1002 ) )D256 - 287
12X-RAY DIFFRACTION10( CHAIN D AND ( RESID 256:287 OR RESID 1001:1002 ) )D1001 - 1002

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