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- PDB-5ywr: Crystal Structure of RING E3 ligase ZNRF1 in complex with Ube2N (... -

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Basic information

Entry
Database: PDB / ID: 5ywr
TitleCrystal Structure of RING E3 ligase ZNRF1 in complex with Ube2N (Ubc13)
Components
  • E3 ubiquitin-protein ligase ZNRF1
  • Ubiquitin-conjugating enzyme E2 N
KeywordsSIGNALING PROTEIN / Ubiquitin E3 ligase / ZNRF1 / Ubiquitin Conjugating E2 / Ube2N / Ubc13
Function / homology
Function and homology information


: / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / positive regulation of double-strand break repair / positive regulation of intracellular signal transduction / E2 ubiquitin-conjugating enzyme ...: / UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / positive regulation of protein K63-linked ubiquitination / DNA double-strand break processing / postreplication repair / positive regulation of double-strand break repair / positive regulation of intracellular signal transduction / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / antiviral innate immune response / protein K48-linked ubiquitination / regulation of DNA repair / ubiquitin ligase complex / negative regulation of TORC1 signaling / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / positive regulation of DNA repair / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / ubiquitin binding / activated TAK1 mediates p38 MAPK activation / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / TAK1-dependent IKK and NF-kappa-B activation / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / G2/M DNA damage checkpoint / ISG15 antiviral mechanism / CLEC7A (Dectin-1) signaling / synaptic vesicle membrane / Formation of Incision Complex in GG-NER / FCERI mediated NF-kB activation / Aggrephagy / Interleukin-1 signaling / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / Processing of DNA double-strand break ends / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / lysosome / protein ubiquitination / endosome / ubiquitin protein ligase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Ring finger domain / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Ring finger / Zinc finger RING-type profile. ...Ring finger domain / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
FORMIC ACID / TRIETHYLENE GLYCOL / Ubiquitin-conjugating enzyme E2 N / E3 ubiquitin-protein ligase ZNRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.47 Å
AuthorsBehera, A.P. / Naskar, P. / Datta, A.B.
Funding support India, 1items
OrganizationGrant numberCountry
Wellcome Trust-DBT India Alliance500241/Z/11/Z India
CitationJournal: Biochem. J. / Year: 2018
Title: Structural insights into the nanomolar affinity of RING E3 ligase ZNRF1 for Ube2N and its functional implications.
Authors: Behera, A.P. / Naskar, P. / Agarwal, S. / Banka, P.A. / Poddar, A. / Datta, A.B.
History
DepositionNov 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2018Provider: 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

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 N
B: E3 ubiquitin-protein ligase ZNRF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5757
Polymers27,1822
Non-polymers3925
Water6,557364
1
A: Ubiquitin-conjugating enzyme E2 N
hetero molecules

B: E3 ubiquitin-protein ligase ZNRF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5757
Polymers27,1822
Non-polymers3925
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area1700 Å2
ΔGint-8 kcal/mol
Surface area13410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.430, 59.548, 94.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / ...Bendless-like ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme N / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17157.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Plasmid: pETSUMO2 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3)
References: UniProt: P61088, E2 ubiquitin-conjugating enzyme
#2: Protein E3 ubiquitin-protein ligase ZNRF1 / Nerve injury-induced gene 283 protein / RING-type E3 ubiquitin transferase ZNRF1 / Zinc/RING finger protein 1


Mass: 10024.536 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: First 137 amino acids deleted from the protein / Source: (gene. exp.) Homo sapiens (human) / Gene: ZNRF1, NIN283 / Plasmid: pETSUMO2 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA2(DE3)
References: UniProt: Q8ND25, RING-type E3 ubiquitin transferase

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Non-polymers , 4 types, 369 molecules

#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: CH2O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.46 Å3/Da / Density % sol: 50.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M Magnesium fromate dihydrate, 20% PEG 3350 (w/v)

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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: Oct 14, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.47→47.43 Å / Num. obs: 46073 / % possible obs: 99.2 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.031 / Net I/σ(I): 20.6
Reflection shellResolution: 1.47→1.5 Å / Rmerge(I) obs: 0.872 / CC1/2: 0.585 / Rpim(I) all: 0.587

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
pointlessdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.47→42.417 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1842 2368 5.15 %
Rwork0.1649 --
obs0.1659 46000 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.47→42.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 16 364 2252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052052
X-RAY DIFFRACTIONf_angle_d0.6832780
X-RAY DIFFRACTIONf_dihedral_angle_d16.219799
X-RAY DIFFRACTIONf_chiral_restr0.075302
X-RAY DIFFRACTIONf_plane_restr0.005370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.50010.34211300.28512269X-RAY DIFFRACTION89
1.5001-1.53270.29911330.2542492X-RAY DIFFRACTION97
1.5327-1.56830.23151210.2242548X-RAY DIFFRACTION100
1.5683-1.60750.21881400.20632558X-RAY DIFFRACTION100
1.6075-1.6510.20141350.19492538X-RAY DIFFRACTION100
1.651-1.69960.21531430.18562572X-RAY DIFFRACTION100
1.6996-1.75450.1991380.18562560X-RAY DIFFRACTION100
1.7545-1.81720.21951410.18242561X-RAY DIFFRACTION100
1.8172-1.88990.17721600.17642531X-RAY DIFFRACTION100
1.8899-1.97590.21721360.17062591X-RAY DIFFRACTION100
1.9759-2.08010.19681360.16192576X-RAY DIFFRACTION100
2.0801-2.21040.17511460.15332594X-RAY DIFFRACTION100
2.2104-2.38110.1571300.15492610X-RAY DIFFRACTION100
2.3811-2.62070.1781310.15772608X-RAY DIFFRACTION100
2.6207-2.99980.18721240.16232629X-RAY DIFFRACTION100
2.9998-3.77910.15111630.14382640X-RAY DIFFRACTION100
3.7791-42.43420.17621610.15182755X-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)
16.93171.5276-0.88588.1536-0.73967.38350.1984-0.44510.15960.5991-0.0430.1483-0.0365-0.0224-0.08080.13620.00020.00650.1077-0.00410.055330.74523.981123.6602
22.79423.1441-3.07354.4238-2.33057.07030.1911-0.23880.40790.3102-0.2451-0.5839-0.07350.4097-0.01350.1393-0.0529-0.01880.1556-0.04230.186137.972833.229318.4815
34.20452.06-2.8292.4014-1.62973.49050.0382-0.12340.0764-0.0544-0.0448-0.1397-0.0660.1655-0.0380.08820.00680.01520.073-0.01560.15233.09236.787510.5088
47.09061.4367-0.14213.4649-3.27613.355-0.0947-0.08750.02-0.18720.06340.49610.3056-0.24260.06880.1204-0.00320.00070.1059-0.0250.141223.680521.113412.6913
50.93120.2834-0.60365.7756-2.63652.51010.01610.11160.079-0.57180.03210.16540.2431-0.135-0.05880.1291-0.0033-0.01050.1066-0.00810.125329.826730.0432.0429
62.7108-0.2789-2.05494.1986-2.06453.05220.16640.4430.0955-0.6509-0.06950.07490.2072-0.3005-0.09070.21360.0261-0.01060.1722-0.0150.175236.185829.37330.374
74.0620.253-0.76094.95091.15994.374-0.0430.32880.3359-0.6754-0.1039-0.2919-0.16850.32280.08650.28690.01510.08580.15920.08930.270337.769243.7774-5.2243
83.4972-1.04742.74542.5058-1.19017.6142-0.07120.2350.08660.0448-0.0274-0.2907-0.15240.21830.07760.1049-0.0083-0.00990.1144-0.01870.165923.03235.7622-4.7667
92.3332-0.48960.60153.7276-0.9384.64750.0194-0.0009-0.1435-0.0727-0.0662-0.20440.16070.27530.01740.05490.0090.01140.0783-0.00330.147332.75396.203915.3719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 27 )
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 57 )
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 67 )
5X-RAY DIFFRACTION5chain 'A' and (resid 68 through 100 )
6X-RAY DIFFRACTION6chain 'A' and (resid 101 through 123 )
7X-RAY DIFFRACTION7chain 'A' and (resid 124 through 152 )
8X-RAY DIFFRACTION8chain 'B' and (resid 141 through 171 ) or chain 'B' and (resid 302)
9X-RAY DIFFRACTION9chain 'B' and (resid 172 through 227) or chain 'B' and (resid 301 and resid 303)

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