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- PDB-1z9l: 1.7 Angstrom Crystal Structure of the Rat VAP-A MSP Homology Domain -

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Basic information

Entry
Database: PDB / ID: 1z9l
Title1.7 Angstrom Crystal Structure of the Rat VAP-A MSP Homology Domain
ComponentsVesicle-associated membrane protein-associated protein A
KeywordsPROTEIN BINDING / VAP-A / Cytoplasmic domain
Function / homology
Function and homology information


FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / sphingomyelin biosynthetic process / ceramide transport / COPII-coated vesicle budding / sterol transport / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation by host of viral genome replication / positive regulation by host of viral genome replication / protein localization to endoplasmic reticulum ...FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / sphingomyelin biosynthetic process / ceramide transport / COPII-coated vesicle budding / sterol transport / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation by host of viral genome replication / positive regulation by host of viral genome replication / protein localization to endoplasmic reticulum / phospholipid transport / cholesterol transport / Neutrophil degranulation / viral release from host cell / bicellular tight junction / endoplasmic reticulum to Golgi vesicle-mediated transport / microtubule cytoskeleton / neuron projection development / microtubule binding / nuclear membrane / vesicle / protein heterodimerization activity / protein domain specific binding / Golgi membrane / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / endoplasmic reticulum / protein homodimerization activity / identical protein binding / membrane / plasma membrane
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 A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsKaiser, S.E. / Brickner, J.H. / Reilein, A.R. / Fenn, T.D. / Walter, P. / Brunger, A.T.
CitationJournal: Structure / Year: 2005
Title: Structural basis of FFAT motif-mediated ER targeting
Authors: Kaiser, S.E. / Brickner, J.H. / Reilein, A.R. / Fenn, T.D. / Walter, P. / Brunger, A.T.
History
DepositionApr 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 A


Theoretical massNumber of molelcules
Total (without water)14,8271
Polymers14,8271
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.200, 48.200, 112.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Vesicle-associated membrane protein-associated protein A / VAMP- associated protein A / VAMP-A / VAP-A / 33 kDa Vamp-associated protein / VAP-33


Mass: 14827.251 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Vapa, Vap33 / Plasmid: pGEX-4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9Z270
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG2000 MME, NaCl, tris buffer, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9795, 0.9793, 0.9649
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 6, 2002
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97931
30.96491
ReflectionResolution: 1.7→50 Å / Num. all: 27524 / Num. obs: 27860 / % possible obs: 98.8 % / Observed criterion σ(F): 8 / Observed criterion σ(I): 8 / Biso Wilson estimate: 17.4 Å2
Reflection shellResolution: 1.7→1.79 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→13.58 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 824290.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2679 9.7 %RANDOM
Rwork0.22 ---
all0.236 27860 --
obs0.22 27484 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.178 Å2 / ksol: 0.365461 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2--0.66 Å20 Å2
3----1.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→13.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1043 0 0 131 1174
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 494 10.7 %
Rwork0.264 4118 -
obs-4118 99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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