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- PDB-5zbu: Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in co... -

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Basic information

Entry
Database: PDB / ID: 5zbu
TitleCrystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub
Components
  • E3 ubiquitin-protein ligase RNF13
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsENDOCYTOSIS / Ubiquitin E3 ligase / PA-TM-RING E3 ligase / RNF13 / E3:E2~Ub complex
Function / homology
Function and homology information


organelle localization / (E3-independent) E2 ubiquitin-conjugating enzyme / JUN kinase binding / nuclear inner membrane / symbiont entry into host cell via disruption of host cell glycocalyx / E2 ubiquitin-conjugating enzyme / symbiont entry into host cell via disruption of host cell envelope / virus tail / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination ...organelle localization / (E3-independent) E2 ubiquitin-conjugating enzyme / JUN kinase binding / nuclear inner membrane / symbiont entry into host cell via disruption of host cell glycocalyx / E2 ubiquitin-conjugating enzyme / symbiont entry into host cell via disruption of host cell envelope / virus tail / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / Inactivation of CSF3 (G-CSF) signaling / positive regulation of JNK cascade / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / RING-type E3 ubiquitin transferase / protein modification process / protein polyubiquitination / ubiquitin-protein transferase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin protein ligase activity / late endosome membrane / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / protein ubiquitination / endosome / lysosomal membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / endoplasmic reticulum / protein-containing complex / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
ZNRF4 /RNF13/RNF167, PA domain / : / Ring finger domain / PA domain superfamily / PA domain / PA domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. ...ZNRF4 /RNF13/RNF167, PA domain / : / Ring finger domain / PA domain superfamily / PA domain / PA domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF13 / Tail fiber / Ubiquitin-conjugating enzyme E2 D2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsDatta, A.B. / Sarkar, S.
Funding support India, 1items
OrganizationGrant numberCountry
Wellcome Trust-DBT India Alliance500241/Z/11/Z India
CitationJournal: To Be Published
Title: Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub
Authors: Sarkar, S. / Datta, A.B.
History
DepositionFeb 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

Downloads & links

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Assembly

Deposited unit
C: Ubiquitin-conjugating enzyme E2 D2
B: Ubiquitin-conjugating enzyme E2 D2
A: E3 ubiquitin-protein ligase RNF13
D: E3 ubiquitin-protein ligase RNF13
E: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1969
Polymers59,9345
Non-polymers2624
Water1629
1
C: Ubiquitin-conjugating enzyme E2 D2
D: E3 ubiquitin-protein ligase RNF13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8104
Polymers25,6792
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin-conjugating enzyme E2 D2
A: E3 ubiquitin-protein ligase RNF13
E: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3865
Polymers34,2563
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.559, 105.740, 60.790
Angle α, β, γ (deg.)90.00, 115.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 D2 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


Mass: 16838.316 Da / Num. of mol.: 2 / Mutation: C85K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Plasmid: pETSUMO2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3)
References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#2: Protein E3 ubiquitin-protein ligase RNF13 / RING finger protein 13 / RING-type E3 ubiquitin transferase RNF13


Mass: 8840.479 Da / Num. of mol.: 2
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
#3: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: P0CG47
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.74 Å3/Da / Density % sol: 55.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M MES monohydrate, 14% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / 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: 3.2→48.71 Å / Num. obs: 10704 / % possible obs: 99.7 % / Redundancy: 3.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.054 / Net I/σ(I): 8.9
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1931 / CC1/2: 0.704 / Rpim(I) all: 0.422 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ESK, 1UBQ

2esk

1ubq


Resolution: 3.2→28.258 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.3
RfactorNum. reflection% reflection
Rfree0.2617 555 5.2 %
Rwork0.2142 --
obs0.2166 10678 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→28.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4150 0 4 9 4163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034253
X-RAY DIFFRACTIONf_angle_d0.665760
X-RAY DIFFRACTIONf_dihedral_angle_d14.9682625
X-RAY DIFFRACTIONf_chiral_restr0.045630
X-RAY DIFFRACTIONf_plane_restr0.005740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.52160.32521880.28062467X-RAY DIFFRACTION100
3.5216-4.02990.3111040.22682553X-RAY DIFFRACTION100
4.0299-5.07250.2441350.20222537X-RAY DIFFRACTION100
5.0725-28.25950.23461280.19962566X-RAY DIFFRACTION99
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)
19.7404-5.2655-2.23082.04652.03713.4132-1.0428-1.1673-1.16280.46890.7926-0.26510.24250.21380.2530.79870.02290.00450.6960.04350.9907-26.96114.38419.4369
28.3218-3.45-4.20364.1573-1.79217.08350.1977-0.12121.6294-0.85710.2787-1.2227-0.29870.5107-0.47350.5584-0.03350.00210.6930.14381.0755-17.14324.8936-0.5008
34.89520.5773-1.08044.5475-0.00274.45340.11071.01771.1147-0.7856-0.1548-0.5974-0.82410.0087-0.07150.91830.07440.23620.5450.22281.0163-24.960411.0753-5.0034
45.05882.71015.80123.15151.14118.90140.9392.52753.12010.14740.69011.73670.27370.7785-0.97821.44140.16610.60321.67760.37811.279-24.75169.1812-18.8851
58.723-6.02490.04458.49291.12953.68441.33011.7041-0.28980.5643-1.43940.3653-1.85882.11070.231.4994-0.08960.12721.62530.15841.1095-18.04766.4419-25.9136
60.8410.00540.79491.998-2.11768.0249-0.16190.9172-1.1431-0.8986-0.365-1.3010.92881.81670.70120.93990.01980.49981.3421-0.02991.6628-10.15780.4573-17.2846
78.11332.52750.74494.25664.73689.4357-0.3004-3.2147-2.40830.1151-0.69651.09470.3348-0.68740.66740.73210.36270.08482.44480.43881.393-24.126334.271212.2571
82.44790.107-1.20030.7623-1.59774.25270.0484-0.62570.86480.32210.06710.20120.3777-0.64190.23951.33240.3874-0.17172.4328-0.2935-0.184-16.771932.992421.2144
97.2575-1.78834.88029.4455-6.07655.77-1.0116-1.42250.47381.5624-0.1813-0.9422-0.7128-0.61730.94240.87590.3070.37261.4538-0.08871.0374-8.952234.003718.3596
105.9485-0.936-3.11.80990.84193.4036-0.4659-1.99550.13351.1874-0.07740.47160.0127-0.4443-0.79151.7550.4194-0.63842.7325-1.82771.08-2.95736.477824.6043
112.83184.59841.29789.57484.1226.46510.5034-2.50840.8339-0.0871-0.1758-2.3968-0.69550.35480.07371.12240.257-0.39982.7078-0.42651.29061.829937.996621.251
127.3478-1.80934.97784.0158-4.35826.33920.3778-0.31580.03850.95061.78950.1531.26191.1729-1.42261.14270.2798-0.24841.4907-0.47310.5785-6.451933.868710.9323
137.4235-0.72045.76172.2073-3.27897.9383-1.2603-0.73040.1488-0.3329-0.4258-1.32561.07961.15451.48561.32980.37310.17282.4234-0.00850.95311.636632.988717.4092
141.069-0.1008-0.99840.20210.22760.9995-0.36650.2787-0.59310.0371-0.66130.1388-1.35260.16180.89981.72560.4688-0.17462.39540.40791.65936.719126.737729.0285
159.57313.63245.98266.88774.91349.4107-1.14540.7087-0.4752-1.81861.2788-0.0153-1.18190.2795-0.2720.9437-0.1371-0.03380.62210.19730.6572-14.989143.4123-12.9914
163.49653.96666.06214.45176.87122.02010.8652-0.1193-1.53920.982-0.4905-1.87912.0828-0.8947-0.3571.036-0.1926-0.26490.94990.00071.9408-26.992927.8453-7.271
174.471-1.97830.22115.6513-1.31719.4504-0.2524-0.58420.2064-0.40660.12050.49460.0733-0.34980.17120.4938-0.0132-0.06980.5675-0.09310.9321-16.482437.1423-5.6266
184.16493.06080.84152.8814-0.68772.86410.76920.07270.8232-4.3521-1.2038-0.6508-0.3614-0.43940.58681.33520.44010.08930.91880.20491.0596-46.442226.4548-2.869
192.4199-2.0731-2.66982.63592.85873.3322-0.9922-1.44240.86520.6099-0.03871.6341-1.8736-2.53780.35080.97050.22090.11211.0255-0.02831.3943-52.8524.85924.2201
202.63560.85132.24452.67370.40087.3393-0.0852-0.3187-0.14910.92750.4923-0.35970.5308-1.3964-0.23040.7313-0.0323-0.02160.69050.18370.9566-51.91127.341510.7568
219.4161-1.3707-0.70444.02113.63494.44141.2308-1.4571.4723-0.2254-0.05550.0263-1.79160.8102-0.65990.7303-0.14650.13440.53730.23020.7024-38.49938.43729.6875
227.0787-3.1383-1.57591.9918.35586.9382-1.5697-1.68790.64642.07610.28961.12242.51480.6570.51821.0758-0.0013-0.02460.77240.31780.5625-46.27225.644916.5445
236.48012.10421.39597.07685.88754.8948-1.92890.4744-0.25710.1518-0.30971.8327-0.83741.63422.06080.7624-0.0616-0.10680.59490.18650.9571-50.710511.41625.5556
243.70523.368-0.22694.00492.34817.13970.96120.40280.91180.0824-0.56251.207-1.0221-0.5128-0.30160.8440.1116-0.16550.5790.14070.8673-43.873417.18186.3523
251.9115-0.1911-3.15042.15542.65237.6204-0.30671.44661.8632-0.27460.3682-0.43520.6109-0.76890.0310.94730.1305-0.1520.80520.15221.0334-45.242115.3868-4.1704
263.41760.1280.34585.20041.17382.1091-0.25080.17110.6599-0.62670.44180.09020.6653-0.03910.17220.5174-0.0418-0.11570.65270.02080.880517.947342.1571-11.8223
276.1303-1.1421.72756.08380.74872.4154-0.4339-0.0694-0.7816-0.6269-0.2173-0.24861.2721-0.29630.78080.73850.14890.07390.8618-0.06320.573414.077540.9812-11.9204
282.2693-4.17813.10327.8142-5.76074.29030.2532-0.67430.5523-1.06460.38910.49462.0251-0.4408-0.76360.7678-0.0638-0.07550.61290.02180.86457.41438.4981-9.3043
299.46094.0224.13662.10323.16037.712-0.428-1.60230.38040.2560.77930.83780.6459-0.5819-0.22460.4993-0.0009-0.02450.76930.05930.4997.076842.468-1.8819
304.15486.44484.76442.00317.42775.4619-1.1097-0.41880.4054-0.5673-0.2551.3313-2.57981.25771.04150.747-0.18950.10740.82710.0950.80688.175752.2862-10.1349
313.9851-1.33723.21392.3955-1.21426.3911-0.4021-0.7536-0.01-0.3792-0.10010.5958-0.2551-0.67740.29810.64150.011-0.04840.6604-0.12390.695812.37246.9462-7.4876
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 0 through 25 )
2X-RAY DIFFRACTION2chain 'C' and (resid 26 through 55 )
3X-RAY DIFFRACTION3chain 'C' and (resid 56 through 111 )
4X-RAY DIFFRACTION4chain 'C' and (resid 112 through 120 )
5X-RAY DIFFRACTION5chain 'C' and (resid 121 through 130 )
6X-RAY DIFFRACTION6chain 'C' and (resid 131 through 147 )
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 15 )
8X-RAY DIFFRACTION8chain 'B' and (resid 16 through 38 )
9X-RAY DIFFRACTION9chain 'B' and (resid 39 through 65 )
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 74 )
11X-RAY DIFFRACTION11chain 'B' and (resid 75 through 84 )
12X-RAY DIFFRACTION12chain 'B' and (resid 85 through 111 )
13X-RAY DIFFRACTION13chain 'B' and (resid 112 through 130 )
14X-RAY DIFFRACTION14chain 'B' and (resid 131 through 146 )
15X-RAY DIFFRACTION15chain 'A' and (resid 216 through 230 )
16X-RAY DIFFRACTION16chain 'A' and (resid 231 through 240 )
17X-RAY DIFFRACTION17chain 'A' and (resid 241 through 289 )
18X-RAY DIFFRACTION18chain 'D' and (resid 215 through 219 )
19X-RAY DIFFRACTION19chain 'D' and (resid 220 through 224 )
20X-RAY DIFFRACTION20chain 'D' and (resid 225 through 240 )
21X-RAY DIFFRACTION21chain 'D' and (resid 241 through 245 )
22X-RAY DIFFRACTION22chain 'D' and (resid 246 through 250 )
23X-RAY DIFFRACTION23chain 'D' and (resid 251 through 260 )
24X-RAY DIFFRACTION24chain 'D' and (resid 261 through 273 )
25X-RAY DIFFRACTION25chain 'D' and (resid 274 through 286 )
26X-RAY DIFFRACTION26chain 'E' and (resid 1 through 7 )
27X-RAY DIFFRACTION27chain 'E' and (resid 8 through 22 )
28X-RAY DIFFRACTION28chain 'E' and (resid 23 through 34 )
29X-RAY DIFFRACTION29chain 'E' and (resid 35 through 44 )
30X-RAY DIFFRACTION30chain 'E' and (resid 45 through 56 )
31X-RAY DIFFRACTION31chain 'E' and (resid 57 through 76 )

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