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Yorodumi- PDB-1hur: HUMAN ADP-RIBOSYLATION FACTOR 1 COMPLEXED WITH GDP, FULL LENGTH N... -
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-Basic information
Entry | Database: PDB / ID: 1hur | ||||||
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Title | HUMAN ADP-RIBOSYLATION FACTOR 1 COMPLEXED WITH GDP, FULL LENGTH NON-MYRISTOYLATED | ||||||
Components | HUMAN ADP-RIBOSYLATION FACTOR 1ARF1 | ||||||
Keywords | PROTEIN TRANSPORT / GDP-BINDING / MEMBRANE TRAFFICKIN / NON-MYRISTOYLATED | ||||||
Function / homology | Function and homology information mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / regulation of receptor internalization / regulation of Arp2/3 complex-mediated actin nucleation / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / Nef Mediated CD4 Down-regulation / dendritic spine organization / long-term synaptic depression / COPI-dependent Golgi-to-ER retrograde traffic ...mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / regulation of receptor internalization / regulation of Arp2/3 complex-mediated actin nucleation / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / Nef Mediated CD4 Down-regulation / dendritic spine organization / long-term synaptic depression / COPI-dependent Golgi-to-ER retrograde traffic / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / cell leading edge / Synthesis of PIPs at the plasma membrane / intracellular copper ion homeostasis / COPI-mediated anterograde transport / vesicle-mediated transport / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / sarcomere / small monomeric GTPase / intracellular protein transport / cellular response to virus / postsynaptic density / neuron projection / protein domain specific binding / Golgi membrane / focal adhesion / GTPase activity / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Amor, J.C. / Harrison, D.H. / Kahn, R.A. / Ringe, D. | ||||||
Citation | Journal: Nature / Year: 1994 Title: Structure of the human ADP-ribosylation factor 1 complexed with GDP. Authors: Amor, J.C. / Harrison, D.H. / Kahn, R.A. / Ringe, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hur.cif.gz | 88.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hur.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 1hur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/1hur ftp://data.pdbj.org/pub/pdb/validation_reports/hu/1hur | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: LYS A 73 - ILE A 74 OMEGA = 124.54 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: PRO A 76 - LEU A 77 OMEGA = 147.30 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
#1: Protein | Mass: 20590.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: HARF1 / Plasmid: PET3 POW12 / Gene (production host): HARF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P84077 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | COMPND MOLECULE: HARF1. MET 1 REMOVED DURING BIOSYNTHES | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.21 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 24, 1993 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 19925 / % possible obs: 82 % / Observed criterion σ(I): 0 / Redundancy: 2.35 % / Rmerge(I) obs: 0.0779 |
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 46853 / Rmerge(I) obs: 0.0779 |
-Processing
Software |
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Refinement | Resolution: 2→15 Å / σ(F): 0 Details: AMINO ACID RESIDUES 70 - 78 ARE RATHER DISORDERED. THEIR INCLUSION IS BASED ON A BEST ESTIMATE FROM FRAGMENTED DIFFERENCE ELECTRON DENSITY. RESIDUE 69 IN BOTH CHAINS ADOPTS AN UNUSUAL PHI- ...Details: AMINO ACID RESIDUES 70 - 78 ARE RATHER DISORDERED. THEIR INCLUSION IS BASED ON A BEST ESTIMATE FROM FRAGMENTED DIFFERENCE ELECTRON DENSITY. RESIDUE 69 IN BOTH CHAINS ADOPTS AN UNUSUAL PHI-PSI TORSION ANGLE. ADDITIONAL REBUILDING AND REFINEMENT HAS NOT IMPROVED THIS SITUATION.
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 19925 / Rfactor all: 0.213 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |