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- PDB-4orh: Crystal structure of RNF8 bound to the UBC13/MMS2 heterodimer -

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Basic information

Entry
Database: PDB / ID: 4orh
TitleCrystal structure of RNF8 bound to the UBC13/MMS2 heterodimer
Components
  • E3 ubiquitin-protein ligase RNF8
  • Ubiquitin-conjugating enzyme E2 N
  • Ubiquitin-conjugating enzyme E2 variant 2
KeywordsPROTEIN BINDING/LIGASE / COILED-COIL / E3 UBIQUITIN LIGASE / UBIQUITIN / PROTEIN BINDING-LIGASE / PROTEIN BINDING-LIGASE complex
Function / homology
Function and homology information


UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / sperm DNA condensation / positive regulation of protein K63-linked ubiquitination / regulation protein catabolic process at postsynapse / DNA double-strand break processing / protein K6-linked ubiquitination / isotype switching / postreplication repair ...UBC13-MMS2 complex / ubiquitin conjugating enzyme complex / ubiquitin-protein transferase activator activity / sperm DNA condensation / positive regulation of protein K63-linked ubiquitination / regulation protein catabolic process at postsynapse / DNA double-strand break processing / protein K6-linked ubiquitination / isotype switching / postreplication repair / E2 ubiquitin-conjugating enzyme / positive regulation of double-strand break repair / response to ionizing radiation / DNA repair-dependent chromatin remodeling / ubiquitin conjugating enzyme activity / negative regulation of transcription elongation by RNA polymerase II / positive regulation of intracellular signal transduction / protein K63-linked ubiquitination / signal transduction in response to DNA damage / protein monoubiquitination / ubiquitin ligase complex / positive regulation of double-strand break repair via homologous recombination / interstrand cross-link repair / regulation of DNA repair / protein K48-linked ubiquitination / protein autoubiquitination / negative regulation of TORC1 signaling / antiviral innate immune response / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of DNA repair / TICAM1, RIP1-mediated IKK complex recruitment / epigenetic regulation of gene expression / ubiquitin binding / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / 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 / G2/M DNA damage checkpoint / NOD1/2 Signaling Pathway / RING-type E3 ubiquitin transferase / double-strand break repair via nonhomologous end joining / ISG15 antiviral mechanism / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Formation of Incision Complex in GG-NER / Interleukin-1 signaling / protein polyubiquitination / Aggrephagy / positive regulation of NF-kappaB transcription factor activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / T cell receptor signaling pathway / site of double-strand break / Processing of DNA double-strand break ends / midbody / ubiquitin-dependent protein catabolic process / histone binding / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / chromosome, telomeric region / postsynapse / protein ubiquitination / cell division / ubiquitin protein ligase binding / DNA damage response / chromatin binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / glutamatergic synapse / protein homodimerization activity / protein-containing complex / RNA binding / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase RNF8 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Zinc finger, C3HC4 type (RING finger) / SMAD/FHA domain superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 ...E3 ubiquitin-protein ligase RNF8 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Zinc finger, C3HC4 type (RING finger) / SMAD/FHA domain superfamily / 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 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / 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 RNF8 / Ubiquitin-conjugating enzyme E2 N / Ubiquitin-conjugating enzyme E2 variant 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.802 Å
AuthorsCampbell, S.J. / Edwards, R.A. / Glover, J.N.M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Molecular insights into the function of RING finger (RNF)-containing proteins hRNF8 and hRNF168 in Ubc13/Mms2-dependent ubiquitylation.
Authors: Campbell, S.J. / Edwards, R.A. / Leung, C.C. / Neculai, D. / Hodge, C.D. / Dhe-Paganon, S. / Glover, J.N.
History
DepositionFeb 11, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 26, 2014ID: 4EPO
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Structure summary
Revision 1.2Dec 3, 2014Group: Structure summary
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 variant 2
B: Ubiquitin-conjugating enzyme E2 N
C: E3 ubiquitin-protein ligase RNF8
E: Ubiquitin-conjugating enzyme E2 variant 2
F: Ubiquitin-conjugating enzyme E2 N
G: E3 ubiquitin-protein ligase RNF8
H: E3 ubiquitin-protein ligase RNF8
I: Ubiquitin-conjugating enzyme E2 variant 2
J: Ubiquitin-conjugating enzyme E2 N
K: E3 ubiquitin-protein ligase RNF8
L: E3 ubiquitin-protein ligase RNF8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,21121
Polymers193,55711
Non-polymers65410
Water00
1
I: Ubiquitin-conjugating enzyme E2 variant 2
J: Ubiquitin-conjugating enzyme E2 N
K: E3 ubiquitin-protein ligase RNF8
L: E3 ubiquitin-protein ligase RNF8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6638
Polymers70,4014
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Ubiquitin-conjugating enzyme E2 variant 2
F: Ubiquitin-conjugating enzyme E2 N
G: E3 ubiquitin-protein ligase RNF8
H: E3 ubiquitin-protein ligase RNF8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6638
Polymers70,4014
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Ubiquitin-conjugating enzyme E2 variant 2
B: Ubiquitin-conjugating enzyme E2 N
C: E3 ubiquitin-protein ligase RNF8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8865
Polymers52,7553
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)205.258, 205.258, 235.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 variant 2 / DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation- ...DDVit 1 / Enterocyte differentiation-associated factor 1 / EDAF-1 / Enterocyte differentiation-promoting factor 1 / EDPF-1 / MMS2 homolog / Vitamin D3-inducible protein


Mass: 17165.590 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMS2, UBE2V2, UEV2 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: Q15819
#2: Protein Ubiquitin-conjugating enzyme E2 N / Bendless-like ubiquitin-conjugating enzyme / Ubc13 / UbcH13 / Ubiquitin carrier protein N / ...Bendless-like ubiquitin-conjugating enzyme / Ubc13 / UbcH13 / Ubiquitin carrier protein N / Ubiquitin-protein ligase N


Mass: 17942.631 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2N, BLU / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: P61088, ubiquitin-protein ligase
#3: Protein
E3 ubiquitin-protein ligase RNF8 / hRNF8 / RING finger protein 8


Mass: 17646.484 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF8, KIAA0646 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold
References: UniProt: O76064, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn

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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: 6.4 Å3/Da / Density % sol: 80.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 75 mM Sodium Acetate, 1.0 M Ammonium Phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.11435 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2011
RadiationMonochromator: Unk. / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11435 Å / Relative weight: 1
ReflectionResolution: 4.8→200 Å / Num. all: 45946 / Num. obs: 45946 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 175.03 Å2 / Rmerge(I) obs: 0.114 / Χ2: 0.985 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
4.8-4.972.30.57344781.077195.8
4.97-5.172.40.53645401.063197.3
5.17-5.412.50.49545751.049197.3
5.41-5.692.50.45945551.035197
5.69-6.052.60.41545241.056196.8
6.05-6.512.80.34845051.025196.3
6.51-7.176.70.51546890.9061100
7.17-8.216.50.25468311100
8.21-10.346.30.09246850.9721100
10.34-20070.04947120.965199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.14data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.802→123.54 Å / FOM work R set: 0.7735 / SU ML: 0.74 / σ(F): 1.91 / Phase error: 31.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2816 1258 5.08 %
Rwork0.2762 --
obs0.2765 45858 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 457.48 Å2 / Biso mean: 258.49 Å2 / Biso min: 175.18 Å2
Refinement stepCycle: LAST / Resolution: 4.802→123.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11418 0 10 0 11428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711728
X-RAY DIFFRACTIONf_angle_d1.09115931
X-RAY DIFFRACTIONf_chiral_restr0.0581817
X-RAY DIFFRACTIONf_plane_restr0.0042084
X-RAY DIFFRACTIONf_dihedral_angle_d12.3614352
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.8018-4.89990.36551300.35492377250792
4.8999-5.00640.36521290.35722566269597
5.0064-5.12290.31011430.3542532267597
5.1229-5.2510.37961470.35442536268397
5.251-5.3930.36941460.3612553269997
5.393-5.55170.36221310.3472525265697
5.5517-5.73080.36231800.33962515269597
5.7308-5.93570.33121180.34122546266497
5.9357-6.17330.32461140.34262543265797
6.1733-6.45430.35331760.35642515269196
6.4543-6.79450.3761240.32692594271899
6.7945-7.22020.36611240.301326182742100
7.2202-7.77760.29561080.278726652773100
7.7776-8.56010.26071510.253626152766100
8.5601-9.79830.2341440.231826152759100
9.7983-12.3430.18931460.18222595274199
12.343-123.58080.21371190.23572618273799
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)
18.80251.5215-1.096810.4676-5.98567.20460.4646-0.10350.5232-0.6378-0.191-0.3261-0.7873-0.102-0.00091.90410.0882-0.41482.7651-0.08822.433446.875333.148217.394
214.3881-4.77162.874615.0554-6.74149.61630.4506-0.402-0.2486-0.3177-0.61730.24580.14-0.53320.00481.1307-0.4525-0.12053.19140.20111.709236.55625.386831.2266
34.6764-1.26841.93244.8112-4.08729.69011.0492-0.65410.44140.3805-0.69240.1681-0.6138-0.2506-0.00021.3826-0.0142-0.35253.5515-0.24343.1576.36568.338630.8612
49.6165-3.2907-1.93928.0628-0.1059.38340.3416-1.956-0.5958-0.292-0.02480.67080.44410.43920.00191.412-0.05240.09583.35930.62462.066293.384-18.978644.8469
59.458-1.5730.714513.17610.953310.3848-0.6477-1.0270.2226-0.0727-0.45870.40980.33210.1613-0.00031.27920.0245-0.01482.8140.63161.884567.2221-1.894634.6389
62.45070.3963-1.9616-1.258-0.53368.15030.5719-0.3301-0.1833-0.13560.1764-0.1134-0.00731.18980.00122.2474-0.11720.16942.52980.03192.360858.0791-14.19120.8909
7-1.08152.72670.09729.3442-7.31695.1519-0.4404-1.02750.1033-0.8789-0.37280.21171.3930.1065-0.02412.256-0.354-0.31352.54340.29382.420345.1038-16.1521-5.3711
8-1.02540.37910.078-0.2201-2.7298-0.90840.4348-0.14082.40922.98290.25212.5559-2.36281.070.24615.00720.59510.73174.566-0.98775.199673.337849.232671.3638
910.60034.007-4.97637.1057-1.865113.6605-0.6813-0.58640.77870.22240.3813-0.5626-0.4983-1.6822-0.00061.54470.7107-0.00983.5799-0.3782.301775.070220.731155.8294
10-0.67451.8203-1.64476.5504-2.21041.3192-0.0041-0.08320.81832.7237-0.2701-0.2449-0.4586-1.382-0.04242.27950.26420.3765.15050.37532.516154.4199-4.038575.0794
110.2624-1.38230.39634.6303-2.0967-1.0143-1.0282-0.9148-0.2838-0.48931.977-0.05830.9064-3.3930.11332.7828-0.3380.46765.16510.66523.075145.9062-15.243870.8316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 144)A0
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 150)B0
3X-RAY DIFFRACTION3(chain 'C' and resid 392 through 483)C0
4X-RAY DIFFRACTION4(chain 'E' and resid 7 through 144)E0
5X-RAY DIFFRACTION5(chain 'F' and resid 3 through 150)F0
6X-RAY DIFFRACTION6(chain 'G' and resid 345 through 483)G0
7X-RAY DIFFRACTION7(chain 'H' and resid 342 through 483)H0
8X-RAY DIFFRACTION8(chain 'I' and resid 7 through 144)I0
9X-RAY DIFFRACTION9(chain 'J' and resid 3 through 150)J0
10X-RAY DIFFRACTION10(chain 'K' and resid 345 through 483)K0
11X-RAY DIFFRACTION11(chain 'L' and resid 342 through 483)L0

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