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- PDB-4oyj: Structure of the apo HOIP PUB domain -

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Basic information

Entry
Database: PDB / ID: 4oyj
TitleStructure of the apo HOIP PUB domain
ComponentsE3 ubiquitin-protein ligase RNF31
KeywordsLIGASE / E3 ubiquitin ligase / PUB domain
Function / homology
Function and homology information


protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / K48-linked polyubiquitin modification-dependent protein binding / TNFR1-induced proapoptotic signaling ...protein linear polyubiquitination / LUBAC complex / linear polyubiquitin binding / CD40 signaling pathway / RBR-type E3 ubiquitin transferase / positive regulation of xenophagy / CD40 receptor complex / negative regulation of necroptotic process / K48-linked polyubiquitin modification-dependent protein binding / TNFR1-induced proapoptotic signaling / positive regulation of protein targeting to mitochondrion / K63-linked polyubiquitin modification-dependent protein binding / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Regulation of TNFR1 signaling / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / defense response to bacterium / ubiquitin protein ligase binding / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2190 / : / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2190 / : / : / : / : / : / E3 ubiquitin-protein ligase RNF31-like / E3 ubiquitin-protein ligase RNF31, UBA-like domain / E3 ubiquitin-protein ligase RNF31, PUB domain / RNF31, C-terminal / HOIP UBA domain pair / E3 Ubiquitin Ligase RBR C-terminal domain / PNGase/UBA- or UBX-containing domain / PUB-like domain superfamily / PUB domain / PUB domain / IBR domain, a half RING-finger domain / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Zinc finger domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF31
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsElliott, P.R. / Komander, D.
CitationJournal: Mol.Cell / Year: 2014
Title: Molecular Basis and Regulation of OTULIN-LUBAC Interaction.
Authors: Elliott, P.R. / Nielsen, S.V. / Marco-Casanova, P. / Fiil, B.K. / Keusekotten, K. / Mailand, N. / Freund, S.M. / Gyrd-Hansen, M. / Komander, D.
History
DepositionFeb 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_symm_contact / refine_hist / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase RNF31
B: E3 ubiquitin-protein ligase RNF31
C: E3 ubiquitin-protein ligase RNF31
D: E3 ubiquitin-protein ligase RNF31
E: E3 ubiquitin-protein ligase RNF31
F: E3 ubiquitin-protein ligase RNF31
G: E3 ubiquitin-protein ligase RNF31
H: E3 ubiquitin-protein ligase RNF31
I: E3 ubiquitin-protein ligase RNF31
J: E3 ubiquitin-protein ligase RNF31
K: E3 ubiquitin-protein ligase RNF31
L: E3 ubiquitin-protein ligase RNF31
M: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,20443
Polymers274,32213
Non-polymers2,88230
Water28816
1
A: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3904
Polymers21,1021
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4865
Polymers21,1021
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4865
Polymers21,1021
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4865
Polymers21,1021
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1982
Polymers21,1021
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3904
Polymers21,1021
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2943
Polymers21,1021
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2943
Polymers21,1021
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3904
Polymers21,1021
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2943
Polymers21,1021
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: E3 ubiquitin-protein ligase RNF31


Theoretical massNumber of molelcules
Total (without water)21,1021
Polymers21,1021
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: E3 ubiquitin-protein ligase RNF31


Theoretical massNumber of molelcules
Total (without water)21,1021
Polymers21,1021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: E3 ubiquitin-protein ligase RNF31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2943
Polymers21,1021
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)155.190, 99.540, 173.730
Angle α, β, γ (deg.)90.00, 99.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
E3 ubiquitin-protein ligase RNF31 / HOIL-1-interacting protein / HOIP / RING finger protein 31 / Zinc in-between-RING-finger ubiquitin- ...HOIL-1-interacting protein / HOIP / RING finger protein 31 / Zinc in-between-RING-finger ubiquitin-associated domain protein / HOIL-1-interacting protein / HOIP / RING finger protein 31 / Zinc in-between-RING-finger ubiquitin-associated domain protein


Mass: 21101.682 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNF31,ZIBRA / Plasmid: pOPINB / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3
References: UniProt: Q96EP0, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.3 M ammonium sulphate, 200 mM KI, 100 mM Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9794 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3→62.75 Å / Num. all: 144088 / Num. obs: 51318 / % possible obs: 98.1 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 6.9
Reflection shellResolution: 3→3.09 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.3 / % possible all: 98.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 3→62.605 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 2542 4.96 %Random selection
Rwork0.207 ---
obs0.2094 51285 97.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→62.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18233 0 150 16 18399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318681
X-RAY DIFFRACTIONf_angle_d0.75325403
X-RAY DIFFRACTIONf_dihedral_angle_d13.8096984
X-RAY DIFFRACTIONf_chiral_restr0.0292876
X-RAY DIFFRACTIONf_plane_restr0.0043363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.05770.32831390.28222706X-RAY DIFFRACTION99
3.0577-3.12010.35471320.27362731X-RAY DIFFRACTION99
3.1201-3.1880.30221490.26162704X-RAY DIFFRACTION98
3.188-3.26210.27481370.24862698X-RAY DIFFRACTION98
3.2621-3.34370.32331500.24192705X-RAY DIFFRACTION99
3.3437-3.43410.30761490.22882710X-RAY DIFFRACTION98
3.4341-3.53510.27081330.21522698X-RAY DIFFRACTION98
3.5351-3.64920.26591330.20842717X-RAY DIFFRACTION98
3.6492-3.77960.2691350.19182719X-RAY DIFFRACTION98
3.7796-3.93090.19821480.18222672X-RAY DIFFRACTION98
3.9309-4.10980.2221480.17822691X-RAY DIFFRACTION98
4.1098-4.32640.23951390.18442702X-RAY DIFFRACTION97
4.3264-4.59740.20311440.16752696X-RAY DIFFRACTION97
4.5974-4.95230.21161200.16832706X-RAY DIFFRACTION97
4.9523-5.45040.24391490.22678X-RAY DIFFRACTION97
5.4504-6.23840.30251630.25142686X-RAY DIFFRACTION97
6.2384-7.85730.27221440.22352737X-RAY DIFFRACTION98
7.8573-62.61870.19471300.1762787X-RAY DIFFRACTION96

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