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- PDB-4cz2: Complex of human VARP-ANKRD1 with Rab32-GppCp. Selenomet derivative. -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cz2 | ||||||
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Title | Complex of human VARP-ANKRD1 with Rab32-GppCp. Selenomet derivative. | ||||||
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![]() | SIGNALING PROTEIN / VARP / RAB-EFFECTOR / RAB / ENDOSOME / VESICLE TRAFFICKING / MELANOSOME BIOGENESIS | ||||||
Function / homology | ![]() 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-lysosome fusion / phagosome maturation / mitochondria-associated endoplasmic reticulum membrane contact site / melanosome assembly ...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-lysosome fusion / phagosome maturation / mitochondria-associated endoplasmic reticulum membrane contact site / melanosome assembly / GTP-dependent protein binding / melanosome membrane / RAB geranylgeranylation / early endosome to late endosome transport / melanosome organization / RAB GEFs exchange GTP for GDP on RABs / protein localization to membrane / endocytic recycling / positive regulation of dendrite morphogenesis / endosome to lysosome transport / antigen processing and presentation / endomembrane system / transport vesicle / phagocytic vesicle / mitochondrion organization / GTPase activator activity / guanyl-nucleotide exchange factor activity / neuron projection morphogenesis / SNARE binding / intracellular protein transport / cytoplasmic vesicle membrane / trans-Golgi network / small GTPase binding / positive regulation of neuron projection development / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Perez-Dorado, I. / Schaefer, I.B. / McCoy, A.J. / Owen, D.J. / Evans, P.R. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 220.2 KB | Display | ![]() |
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PDB format | ![]() | 174.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 40.3 KB | Display | |
Data in CIF | ![]() | 54 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cymSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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5 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() #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 | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.4 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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.
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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
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Refinement step | Cycle: LAST / Resolution: 2.97→120.89 Å
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Refine LS restraints |
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