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- PDB-2o95: Crystal Structure of the Metal-Free Dimeric Human Mov34 MPN domai... -

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Basic information

Entry
Database: PDB / ID: 2o95
TitleCrystal Structure of the Metal-Free Dimeric Human Mov34 MPN domain (residues 1-186)
Components26S proteasome non-ATPase regulatory subunit 7
KeywordsUNKNOWN FUNCTION / PSMD7 / 26S Proteasome / Mov34 / Jab1/MPN / metal-free dimer
Function / homology
Function and homology information


proteasome regulatory particle / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 ...proteasome regulatory particle / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of AXIN / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Negative regulation of NOTCH4 signaling / G2/M Checkpoints / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / UCH proteinases / The role of GTSE1 in G2/M progression after G2 checkpoint / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / ficolin-1-rich granule lumen / Ub-specific processing proteases / Neutrophil degranulation / protein homodimerization activity / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. ...Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ETE / TRIETHYLENE GLYCOL / 26S proteasome non-ATPase regulatory subunit 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsSanches, M. / Alves, B.S.C. / Zanchin, N.I.T. / Guimaraes, B.G.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: The Crystal Structure of the Human Mov34 MPN Domain Reveals a Metal-free Dimer
Authors: Sanches, M. / Alves, B.S.C. / Zanchin, N.I.T. / Guimaraes, B.G.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 2006
Title: Characterization of the human ortholog of Mov34 reveals eight N-terminal residues important for MPN domain stability
Authors: Alves, B.S.C. / Oyama Jr., S. / Gozzo, F.C. / Sanches, M. / Guimaraes, B.G. / Zanchin, N.I.T.
History
DepositionDec 13, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: 26S proteasome non-ATPase regulatory subunit 7
B: 26S proteasome non-ATPase regulatory subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,00012
Polymers42,1622
Non-polymers1,83810
Water5,765320
1
A: 26S proteasome non-ATPase regulatory subunit 7
hetero molecules

A: 26S proteasome non-ATPase regulatory subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,43712
Polymers42,1622
Non-polymers2,27510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area6540 Å2
ΔGint-40 kcal/mol
Surface area17710 Å2
MethodPISA, PQS
2
B: 26S proteasome non-ATPase regulatory subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7826
Polymers21,0811
Non-polymers7015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-48 kcal/mol
Surface area21210 Å2
MethodPISA
4
B: 26S proteasome non-ATPase regulatory subunit 7
hetero molecules

B: 26S proteasome non-ATPase regulatory subunit 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,56312
Polymers42,1622
Non-polymers1,40110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)114.103, 95.289, 58.988
Angle α, β, γ (deg.)90.000, 121.130, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 1 / Auth seq-ID: 1 - 181 / Label seq-ID: 2 - 182

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological assembly is a dimer generated by the symmetry operation -x y -z. The asymmetric unit contains a dimmer which does not represent the biological assembly.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome regulatory subunit rpn8 / 26S proteasome regulatory subunit S12 / Proteasome subunit ...26S proteasome regulatory subunit rpn8 / 26S proteasome regulatory subunit S12 / Proteasome subunit p40 / Mov34 protein homolog


Mass: 21080.977 Da / Num. of mol.: 2 / Fragment: MPN domain, N-terminus domain, residues 1-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD7, Mov34L / Plasmid: pET28a-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)slyD- / References: UniProt: P51665

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Non-polymers , 6 types, 330 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O5
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 3.25 Å3/Da / Density % sol: 62.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1M phosphate-citrate buffer, 20% PEG 1000, 0.2M LiSO4, 10mM MnCl2 as additive, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 6, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 1.95→68.205 Å / Num. all: 49805 / Num. obs: 39272 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.6 / Redundancy: 3.3 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 11.9
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 1.6 / Num. measured all: 17623 / Num. unique all: 5682 / Rsym value: 0.476 / % possible all: 99.5

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Phasing

PhasingMethod: SAD
Phasing MAD set
IDR cullis acentricR cullis centricHighest resolution (Å)Lowest resolution (Å)Reflection acentricReflection centric
ISO_1002.135.04307681007
ANO_10.77202.135.04307620
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricReflection acentricReflection centric
ISO_19.09-35.040035551
ISO_16.54-9.090062549
ISO_15.37-6.540080350
ISO_14.66-5.370095249
ISO_14.18-4.6600110253
ISO_13.82-4.1800121646
ISO_13.54-3.8200129950
ISO_13.31-3.5400142649
ISO_13.12-3.3100147150
ISO_12.96-3.1200158052
ISO_12.83-2.9600171246
ISO_12.71-2.8300174355
ISO_12.6-2.7100182650
ISO_12.51-2.600190057
ISO_12.42-2.5100196349
ISO_12.35-2.4200202743
ISO_12.28-2.3500206853
ISO_12.21-2.2800219255
ISO_12.15-2.2100221045
ISO_12.1-2.1500229855
ANO_19.09-35.040.44903490
ANO_16.54-9.090.46206250
ANO_15.37-6.540.45608030
ANO_14.66-5.370.47909520
ANO_14.18-4.660.549011020
ANO_13.82-4.180.59012160
ANO_13.54-3.820.642012990
ANO_13.31-3.540.695014260
ANO_13.12-3.310.75014710
ANO_12.96-3.120.811015800
ANO_12.83-2.960.858017120
ANO_12.71-2.830.903017430
ANO_12.6-2.710.928018260
ANO_12.51-2.60.961019000
ANO_12.42-2.510.978019630
ANO_12.35-2.420.989020270
ANO_12.28-2.350.994020680
ANO_12.21-2.280.998021920
ANO_12.15-2.210.998022100
ANO_12.1-2.151.001022980
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-44.464-5.845-15.545I60.020.99
2-49.3180.29-7.778I58.380.95
39.932-40.396-16.635I63.690.5
4-30.003-13.906-41.539I84.290.64
5-6.07-47.168-7.779I48.250.36
6-22.969-7.368-26.857I45.080.25
7-30.833-7.168-23.244I52.160.38
8-6.418-46.79-16.615I48.710.25
919.957-33.912-39.007I65.060.28

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
SHARPphasing
SOLOMONphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.95→30.21 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.712 / SU ML: 0.101 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.148 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1973 5 %RANDOM
Rwork0.201 ---
all0.203 39262 --
obs0.203 37289 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.953 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.05 Å2
2---0.31 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 0 118 320 3283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223037
X-RAY DIFFRACTIONr_angle_refined_deg2.051.9814099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3725368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.07925.692130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29915496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.733156
X-RAY DIFFRACTIONr_chiral_restr0.140.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022198
X-RAY DIFFRACTIONr_nbd_refined0.2610.21945
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22066
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2354
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.2187
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.231
X-RAY DIFFRACTIONr_mcbond_it0.8691.51858
X-RAY DIFFRACTIONr_mcangle_it1.32722968
X-RAY DIFFRACTIONr_scbond_it2.54231308
X-RAY DIFFRACTIONr_scangle_it3.3454.51129
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1362 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.090.05
TIGHT THERMAL0.280.5
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 151 -
Rwork0.322 2744 -
obs-2895 99.42 %

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