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- PDB-3gf5: Crystal structure of the P21 R1-R7 N-terminal domain of murine MVP -

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Basic information

Entry
Database: PDB / ID: 3gf5
TitleCrystal structure of the P21 R1-R7 N-terminal domain of murine MVP
ComponentsMajor vault protein
KeywordsSTRUCTURAL PROTEIN / beta sheets / Phosphoprotein / Ribonucleoprotein
Function / homology
Function and homology information


protein activation cascade / negative regulation of protein autophosphorylation / ERBB signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / Neutrophil degranulation / protein phosphatase binding / cell population proliferation / cytoskeleton / ribonucleoprotein complex / protein kinase binding ...protein activation cascade / negative regulation of protein autophosphorylation / ERBB signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / Neutrophil degranulation / protein phosphatase binding / cell population proliferation / cytoskeleton / ribonucleoprotein complex / protein kinase binding / perinuclear region of cytoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Major vault protein, N-terminal structural repeat domain / SH3 type barrels. - #570 / Major Vault Protein repeat / Major vault protein, N-terminal / Major vault protein, shoulder domain / Major vault protein / Major vault protein repeat domain 3 / Major vault protein repeat domain 2 / Major vault protein repeat domain 4 / Major vault protein repeat domain ...Major vault protein, N-terminal structural repeat domain / SH3 type barrels. - #570 / Major Vault Protein repeat / Major vault protein, N-terminal / Major vault protein, shoulder domain / Major vault protein / Major vault protein repeat domain 3 / Major vault protein repeat domain 2 / Major vault protein repeat domain 4 / Major vault protein repeat domain / Major vault protein repeat domain superfamily / Major vault protein repeat domain 2 superfamily / Major Vault Protein repeat domain / Shoulder domain / Major Vault Protein repeat domain / Major Vault Protein Repeat domain / Major Vault Protein repeat domain / MVP (vault) repeat profile. / Band 7/SPFH domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsQuerol-Audi, J. / Casanas, A. / Luque, D. / Caston, J.R. / Fita, I. / Verdaguer, N.
CitationJournal: Embo J. / Year: 2009
Title: The mechanism of vault opening from the high resolution structure of the N-terminal repeats of MVP
Authors: Querol-Audi, J. / Casanas, A. / Uson, I. / Luque, D. / Caston, J.R. / Fita, I. / Verdaguer, N.
History
DepositionFeb 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Major vault protein
B: Major vault protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1169
Polymers87,4722
Non-polymers6457
Water81145
1
A: Major vault protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9203
Polymers43,7361
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Major vault protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1966
Polymers43,7361
Non-polymers4605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.523, 98.892, 140.581
Angle α, β, γ (deg.)90.000, 97.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Major vault protein / MVP


Mass: 43735.777 Da / Num. of mol.: 2 / Fragment: R1-R7 domain, UNP residues 1-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: MVP / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9EQK5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% PEG 5000, 0.1M Sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979,0.976
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 12, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9761
ReflectionResolution: 2.5→30 Å / Num. all: 34051 / Num. obs: 33339 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.1
Reflection shellResolution: 2.5→2.565 Å / % possible all: 81.84

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
DMphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MAD / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.6 / SU B: 23.109 / SU ML: 0.239 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.546 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26691 1677 5 %RANDOM
Rwork0.23155 ---
obs0.2333 31662 96.9 %-
all-34051 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å2-0.04 Å2
2---1 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6008 0 42 45 6095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0226173
X-RAY DIFFRACTIONr_bond_other_d0.0010.024239
X-RAY DIFFRACTIONr_angle_refined_deg0.9121.9778380
X-RAY DIFFRACTIONr_angle_other_deg0.706310335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6875754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68224.141297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.617151053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4681552
X-RAY DIFFRACTIONr_chiral_restr0.0560.2947
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026806
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021182
X-RAY DIFFRACTIONr_nbd_refined0.1740.21054
X-RAY DIFFRACTIONr_nbd_other0.1640.24262
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22950
X-RAY DIFFRACTIONr_nbtor_other0.0760.23479
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2139
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1730.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1931.54733
X-RAY DIFFRACTIONr_mcbond_other0.0261.51514
X-RAY DIFFRACTIONr_mcangle_it0.2426151
X-RAY DIFFRACTIONr_scbond_it0.39232647
X-RAY DIFFRACTIONr_scangle_it0.584.52229
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 106 -
Rwork0.415 1985 -
obs--81.84 %
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)
15.60060.9547-0.84364.58682.51299.77440.1963-0.45960.02410.3517-0.0205-0.0615-0.0830.0512-0.1757-0.0947-0.0150.0112-0.284-0.0247-0.09846.37317.973697.9754
21.5578-0.27051.65682.45731.38027.1579-0.09810.1057-0.00140.03280.0701-0.3367-0.24270.38770.028-0.16740.06240.0223-0.138-0.05230.03298.320511.157179.9593
310.1234-0.62461.99622.4589-2.172510.3823-0.0134-0.33630.1936-0.1949-0.264-0.4951-0.16420.8490.2774-0.1370.1160.00410.0817-0.085-0.05327.61259.009258.9465
45.036-1.60433.20890.6185-0.022211.3532-0.1225-0.12120.40270.00110.139-0.08130.31580.4217-0.0164-0.07780.08550.0136-0.14220.0422-0.028-0.331810.288637.567
57.3638-0.00484.31652.5148-0.65989.5020.0039-0.1174-0.5609-0.08940.0709-0.04710.55360.2963-0.07490.02990.07350.0944-0.2520.0077-0.048-4.525510.560817.4236
64.76921.76781.89344.6991-2.167813.84980.4512-0.1332-0.3861-0.8412-0.1294-0.16790.57260.5466-0.32170.28220.16360.0716-0.1669-0.0041-0.0309-10.261113.3684-2.5837
79.8105-0.6193-2.82727.6544-0.437914.2737-0.38860.3172-0.5405-0.05870.3290.18651.114-0.11610.05960.38730.033-0.0494-0.0774-0.0048-0.1023-14.294814.1869-22.1679
83.06380.81210.14373.1606-2.661410.14270.137-0.2547-0.1630.55710.03640.1831-0.0769-0.0658-0.1734-0.19820.01410.0386-0.106-0.0113-0.1208-3.7122-19.2758122.7555
95.08880.8873-5.21120.8051-1.98913.52140.14140.39710.48220.30260.09570.2666-0.6777-0.9108-0.2371-0.28510.06910.0174-0.03230.0223-0.0481-4.4197-11.6164104.9966
1012.526-3.17-2.68553.25610.64725.76260.132-0.44420.1194-0.112-0.04690.3278-0.1525-0.6826-0.0851-0.41930.0631-0.03730.07540.0395-0.1645-3.4951-9.194684.2262
113.6683-2.9388-1.62612.36261.601611.4397-0.1321-0.3542-0.1131-0.06840.02080.0023-0.2637-0.35710.1112-0.27740.0156-0.0474-0.0393-0.0419-0.10673.7352-10.198862.4812
125.0492-3.1577-3.20764.2931.98610.48310.0145-0.24670.2668-0.2670.1835-0.0361-0.3176-0.1641-0.198-0.1767-0.0108-0.0436-0.27240.0048-0.17877.5554-10.509842.2997
137.32660.1613-4.19712.60612.463312.03060.21040.3270.5313-0.5650.01690.1547-0.177-0.3825-0.22730.2964-0.0211-0.0717-0.26070.0503-0.108712.6461-14.09722.1249
1411.11070.00923.71785.39620.152215.3448-0.10490.55240.52640.2205-0.0551-0.2885-1.2224-0.20890.160.3689-0.0320.1145-0.10310.0373-0.165916.3199-15.26382.6246
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 53
2X-RAY DIFFRACTION2A56 - 115
3X-RAY DIFFRACTION3A118 - 163
4X-RAY DIFFRACTION4A164 - 221
5X-RAY DIFFRACTION5A222 - 276
6X-RAY DIFFRACTION6A279 - 326
7X-RAY DIFFRACTION7A328 - 380
8X-RAY DIFFRACTION8B1 - 53
9X-RAY DIFFRACTION9B56 - 115
10X-RAY DIFFRACTION10B118 - 163
11X-RAY DIFFRACTION11B164 - 221
12X-RAY DIFFRACTION12B222 - 276
13X-RAY DIFFRACTION13B279 - 326
14X-RAY DIFFRACTION14B328 - 380

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