[English] 日本語
Yorodumi- PDB-4cz2: Complex of human VARP-ANKRD1 with Rab32-GppCp. Selenomet derivative. -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cz2 | ||||||
---|---|---|---|---|---|---|---|
Title | Complex of human VARP-ANKRD1 with Rab32-GppCp. Selenomet derivative. | ||||||
Components |
| ||||||
Keywords | SIGNALING PROTEIN / VARP / RAB-EFFECTOR / RAB / ENDOSOME / VESICLE TRAFFICKING / MELANOSOME BIOGENESIS | ||||||
Function / homology | Function and homology information BLOC-2 complex binding / AP-3 adaptor complex binding / AP-1 adaptor complex binding / negative regulation of SNARE complex assembly / tubular endosome / endosome to melanosome transport / phagosome maturation / mitochondria-associated endoplasmic reticulum membrane contact site / melanosome assembly / melanosome organization ...BLOC-2 complex binding / AP-3 adaptor complex binding / AP-1 adaptor complex binding / negative regulation of SNARE complex assembly / tubular endosome / endosome to melanosome transport / phagosome maturation / mitochondria-associated endoplasmic reticulum membrane contact site / melanosome assembly / melanosome organization / melanosome membrane / GTP-dependent protein binding / RAB geranylgeranylation / early endosome to late endosome transport / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / protein localization to membrane / positive regulation of dendrite morphogenesis / antigen processing and presentation / endomembrane system / phagocytic vesicle / transport vesicle / vesicle-mediated transport / mitochondrion organization / GTPase activator activity / SNARE binding / guanyl-nucleotide exchange factor activity / neuron projection morphogenesis / intracellular protein transport / trans-Golgi network / cytoplasmic vesicle membrane / positive regulation of neuron projection development / small GTPase binding / phagocytic vesicle membrane / melanosome / protein transport / late endosome / mitochondrial outer membrane / lysosome / early endosome / neuron projection / intracellular membrane-bounded organelle / GTPase activity / GTP binding / endoplasmic reticulum / mitochondrion / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å | ||||||
Authors | Perez-Dorado, I. / Schaefer, I.B. / McCoy, A.J. / Owen, D.J. / Evans, P.R. | ||||||
Citation | Journal: Dev.Cell / Year: 2014 Title: Varp is Recruited on to Endosomes by Direct Interaction with Retromer, Where Together They Function in Export to the Cell Surface. Authors: Hesketh, G.G. / Perez-Dorado, I. / Jackson, L.P. / Wartosch, L. / Schefer, I.B. / Gray, S.R. / Mccoy, A.J. / Zeldin, O.B. / Garman, E.F. / Harbour, M.E. / Evans, P.R. / Seaman, M.N. / Luzio, J.P. / Owen, D.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4cz2.cif.gz | 220.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4cz2.ent.gz | 174.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/4cz2 ftp://data.pdbj.org/pub/pdb/validation_reports/cz/4cz2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4cymSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||
3 |
| ||||||||||||||||||||||||||||
4 |
| ||||||||||||||||||||||||||||
5 |
| ||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||
Components on special symmetry positions |
| ||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 25792.365 Da / Num. of mol.: 3 / Fragment: RESIDUES 450-640 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q13637 #2: Protein | Mass: 22312.137 Da / Num. of mol.: 3 Fragment: FIRST ANKYRIN REPEAT-CONTAINING DOMAIN, RESIDUES 1-225 Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q96NW4 #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | NTERMINAL SEQUENCE GPLGSM IS AN INSERTION COMING FROM THE EXPRESSION PLASMID USED. GLN 85 WAS ...NTERMINAL SEQUENCE GPLGSM IS AN INSERTION COMING FROM THE EXPRESSION | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.4 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→57.05 Å / Num. obs: 33062 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.97→3.12 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.9 / % possible all: 98.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CYM Resolution: 2.97→120.89 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.89 / SU B: 18.406 / SU ML: 0.308 / Cross valid method: THROUGHOUT / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MISSING RESIDUES. RESIDUES 1-21, 149-152 AND 198-225 OF CHAIN A. RESIDUES 1-20 AND 199-225 OF CHAIN B. RESIDUES 1- 21, 149-152 AND 198-225 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MISSING RESIDUES. RESIDUES 1-21, 149-152 AND 198-225 OF CHAIN A. RESIDUES 1-20 AND 199-225 OF CHAIN B. RESIDUES 1- 21, 149-152 AND 198-225 OF CHAIN C. RESIDUES 450-452 AND 621-640 OF CHAIN D. RESIDUES 450-452 AND 619-640 OF CHAIN E. RESIDUES 450-453 AND 619-640 OF CHAIN F. RESIDUES FROM - 5 TO 0. CTERMINAL HIS-TAGS IN CHAINS D, E AND F.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.665 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.97→120.89 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|