[English] 日本語
Yorodumi
- PDB-1z9l: 1.7 Angstrom Crystal Structure of the Rat VAP-A MSP Homology Domain -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more