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- PDB-2o96: Crystal Structure of the Metal-Free Dimeric Human Mov34 MPN domai... -

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Basic information

Entry
Database: PDB / ID: 2o96
TitleCrystal Structure of the Metal-Free Dimeric Human Mov34 MPN domain (residues 1-177)
Components26S proteasome non-ATPase regulatory subunit 7
KeywordsUNKNOWN FUNCTION / PSMD7 / 26S Proteasome subunit / 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 / Hedgehog ligand biogenesis / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / 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 / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / 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
26S proteasome non-ATPase regulatory subunit 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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: Advisory / Version format compliance
Revision 1.3Oct 25, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 26S proteasome non-ATPase regulatory subunit 7
B: 26S proteasome non-ATPase regulatory subunit 7


Theoretical massNumber of molelcules
Total (without water)40,2982
Polymers40,2982
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-18 kcal/mol
Surface area16810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.701, 96.010, 60.982
Angle α, β, γ (deg.)90.000, 122.140, 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: PRO / Beg label comp-ID: PRO / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth seq-ID: 2 - 167 / Label seq-ID: 3 - 168

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological assembly is a dimer in the asymetric unit.

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Components

#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: 20148.967 Da / Num. of mol.: 2 / Fragment: MPN domain, N-terminus domain, residues 1-177
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M citrate, 0,2M NH4OAc, 30% PEG 4000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
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: 3→68.278 Å / Num. all: 13093 / Num. obs: 10578 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.3 / Redundancy: 3 % / Biso Wilson estimate: 76.858 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3-3.162.90.5621.3456215470.56296.3
3.16-3.3530.3062.4441814840.30695.4
3.35-3.5930.1754.2418313980.17595.1
3.59-3.8730.1215.9386012740.12194.5
3.87-4.243.10.0858.3360011800.08593.8
4.24-4.743.10.05912.1322310550.05993.1
4.74-5.483.10.05313.428709280.05392.8
5.48-6.713.10.0591224918000.05991.8
6.71-9.493.20.03318.818545880.03389.7
9.49-51.653.20.02719.810253240.02786.9

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3 Å51.65 Å
Translation3 Å51.65 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O95

2o95


Resolution: 3→51.64 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.874 / SU B: 29.805 / SU ML: 0.256 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.408 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 509 4.8 %RANDOM
Rwork0.204 ---
all0.206 10577 --
obs0.206 10068 93.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.481 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20.27 Å2
2--0.04 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 3→51.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2557 0 0 0 2557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222613
X-RAY DIFFRACTIONr_angle_refined_deg1.591.953536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1725313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65725.041121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.47115463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8091510
X-RAY DIFFRACTIONr_chiral_restr0.1010.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021934
X-RAY DIFFRACTIONr_nbd_refined0.2670.21307
X-RAY DIFFRACTIONr_nbtor_refined0.3280.21776
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2110
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0190.22
X-RAY DIFFRACTIONr_mcbond_it1.4321.51621
X-RAY DIFFRACTIONr_mcangle_it2.54322584
X-RAY DIFFRACTIONr_scbond_it1.91431115
X-RAY DIFFRACTIONr_scangle_it3.1754.5952
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1268 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.040.05
TIGHT THERMAL0.060.5
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 40 -
Rwork0.285 737 -
obs-777 96.64 %
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)
14.39553.10620.29862.3629-0.80516.17320.2155-0.6812-0.16140.8301-0.0005-0.33060.62990.5017-0.2150.1235-0.1104-0.01670.2892-0.01910.281424.846611.418-2.9856
25.39312.6255-0.3536138.5937-21.80783.43222.7220.27890.4403-6.6948-2.20072.6023-0.55461.1292-0.52131.04560.4120.16290.6848-0.10930.57129.53660.6249-20.3625
32.65871.0908-0.24860.7506-0.79199.99520.2251-0.0371-0.09010.03580.06-0.0237-0.0496-0.1245-0.28510.2689-0.00820.03650.269-0.01830.300919.681613.1668-11.92
44.03621.6035-0.45283.8112-0.75590.9085-0.04120.06990.09020.1820.082-0.0044-0.15170.064-0.04080.32920.0011-0.00130.3168-0.01420.259216.241112.8589-10.3717
5187.04914.588972.36361.36449.182283.25122.0783-2.6723-4.1861-0.9256-1.74724.5244-2.33382.8992-0.33110.3130.07770.06890.3532-0.10391.385538.60487.8647-10.2204
69.0325-6.55764.442211.7061-6.502211.10120.1954-0.40930.3197-0.1710.0144-0.0188-0.21260.4028-0.20980.1906-0.1304-0.05120.3072-0.11310.259225.18320.8039-4.4109
76.5280.8442-0.4714.1236-3.84223.59570.1113-0.03820.5824-0.4242-0.111-0.5573-0.24060.7171-0.00030.17210.0412-0.09480.31460.05910.134124.643-13.2193-2.4646
8000000-0.138-0.40324.28561.8870.25392.61931.95960.6085-0.11590.9613-0.28020.59330.6752-0.10921.969510.7016-1.44849.6623
96.1505-0.1761-0.81581.3061-1.50082.5911-0.04910.0710.39590.0360.0986-0.05150.0444-0.1292-0.04940.31420.0155-0.0140.2681-0.03090.220914.0447-13.9922-2.9474
101.74640.07811.68813.4002-1.153.5248-0.0836-0.0103-0.1321-0.16830.1458-0.12630.0815-0.0789-0.06220.27870.03420.02620.3047-0.01580.327613.7959-13.7333-7.0132
114.0964-2.23430.670912.95393.156.97920.2373-0.6467-0.33771.11320.2805-0.21720.91580.453-0.51780.31150.0735-0.030.34120.08130.271420.2708-22.1592.7526
121.54864.35590.258713.55674.00198.2626-0.31360.1597-0.4425-0.35020.7498-3.1248-1.65310.0783-0.43620.39440.0343-0.06140.7405-0.03760.579234.1675-8.3819-2.9313
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 243 - 25
22AA25 - 3326 - 34
33AA34 - 6935 - 70
44AA70 - 12571 - 126
55AA126 - 130127 - 131
66AA133 - 167134 - 168
77BB1 - 242 - 25
88BB25 - 3326 - 34
99BB34 - 6935 - 70
1010BB70 - 12471 - 125
1111BB125 - 158126 - 159
1212BB159 - 168160 - 169

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