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- PDB-3ikk: Crystal structure analysis of msp domain -

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Basic information

Entry
Database: PDB / ID: 3ikk
TitleCrystal structure analysis of msp domain
ComponentsVesicle-associated membrane protein-associated protein B/C
KeywordsMEMBRANE PROTEIN / VAPB MSP / Alternative splicing / Amyotrophic lateral sclerosis / Cell membrane / Coiled coil / Disease mutation / Host-virus interaction / Membrane / Neurodegeneration / Phosphoprotein / Transmembrane
Function / homology
Function and homology information


negative regulation by virus of viral protein levels in host cell / endoplasmic reticulum membrane organization / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / modulation by host of viral RNA genome replication / suppression of viral release by host / COPII-coated vesicle budding / negative regulation by host of viral genome replication / positive regulation by host of viral genome replication / Sphingolipid de novo biosynthesis ...negative regulation by virus of viral protein levels in host cell / endoplasmic reticulum membrane organization / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / modulation by host of viral RNA genome replication / suppression of viral release by host / COPII-coated vesicle budding / negative regulation by host of viral genome replication / positive regulation by host of viral genome replication / Sphingolipid de novo biosynthesis / cholesterol transport / endoplasmic reticulum organization / RHOD GTPase cycle / beta-tubulin binding / IRE1-mediated unfolded protein response / RHOC GTPase cycle / viral release from host cell / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / positive regulation of viral genome replication / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum unfolded protein response / intracellular calcium ion homeostasis / microtubule binding / cadherin binding / protein heterodimerization activity / endoplasmic reticulum membrane / Golgi apparatus / enzyme binding / endoplasmic reticulum / protein homodimerization activity / plasma membrane / cytoplasm
Similarity search - Function
Vesicle-associated membrane-protein-associated protein / Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / PapD-like superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Vesicle-associated membrane protein-associated protein B/C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShi, J. / Lua, S. / Song, J.
CitationJournal: Biochemistry / Year: 2010
Title: Elimination of the native structure and solubility of the hVAPB MSP domain by the Pro56Ser mutation that causes amyotrophic lateral sclerosis.
Authors: Shi, J. / Lua, S. / Tong, J.S. / Song, J.
History
DepositionAug 6, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vesicle-associated membrane protein-associated protein B/C
B: Vesicle-associated membrane protein-associated protein B/C


Theoretical massNumber of molelcules
Total (without water)28,7212
Polymers28,7212
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-4 kcal/mol
Surface area14390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.024, 144.024, 34.791
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Vesicle-associated membrane protein-associated protein B/C / Human VAP-B MSP Domain / VAMP-associated protein B/C / VAMP-B/VAMP-C / VAP-B/VAP-C


Mass: 14360.489 Da / Num. of mol.: 2 / Fragment: VAPB msp domain, UNP residues 1-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UNQ484/PRO983, VAPB / Plasmid: PET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O95292
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 200mM Ammonium acetate, 25% PEG3350, 0.1M Tril-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Aug 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.137
ReflectionResolution: 2.5→72 Å / Num. all: 9306 / Num. obs: 9305 / % possible obs: 100 % / Redundancy: 17.41 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.3024 / Rsym value: 0.104 / Net I/σ(I): 8.64
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 14.99 % / Rmerge(I) obs: 0.8953 / Mean I/σ(I) obs: 1.29 / Num. unique all: 927 / Rsym value: 0.776 / % possible all: 100

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASESphasing
PHENIXrefinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z9L

1z9l


Resolution: 2.5→41.576 Å / Cross valid method: THROUGHOUT / σ(F): 0.12 / Phase error: 31.21 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2655 935 10.33 %RANDOM
Rwork0.2068 ---
obs0.2129 9055 97.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.517 Å2 / ksol: 0.369 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.2979 Å20 Å20 Å2
2--7.2979 Å20 Å2
3----14.5958 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 0 73 2057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082027
X-RAY DIFFRACTIONf_angle_d1.2692738
X-RAY DIFFRACTIONf_dihedral_angle_d20.661776
X-RAY DIFFRACTIONf_chiral_restr0.076306
X-RAY DIFFRACTIONf_plane_restr0.008356
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5015-2.63340.31281250.2638107281
2.6334-2.79830.32911230.2285113185
2.7983-3.01430.27481300.233116088
3.0143-3.31750.30381320.2041118589
3.3175-3.79730.28731310.193120890
3.7973-4.78310.22691380.1824119390
4.7831-41.58190.22131320.206118290

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