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Yorodumi- PDB-3a4u: Crystal structure of MCFD2 in complex with carbohydrate recogniti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a4u | ||||||
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Title | Crystal structure of MCFD2 in complex with carbohydrate recognition domain of ERGIC-53 | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / LECTIN / ERGIC / ER / GOLGI / TRANSPORT / Disulfide bond / Endoplasmic reticulum / ER-Golgi transport / Golgi apparatus / Membrane / Transmembrane / Disease mutation | ||||||
Function / homology | Function and homology information Transport to the Golgi and subsequent modification / positive regulation of organelle organization / negative regulation of protein targeting to mitochondrion / Cargo concentration in the ER / RHOD GTPase cycle / endoplasmic reticulum organization / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / RHOC GTPase cycle / Golgi organization ...Transport to the Golgi and subsequent modification / positive regulation of organelle organization / negative regulation of protein targeting to mitochondrion / Cargo concentration in the ER / RHOD GTPase cycle / endoplasmic reticulum organization / COPII-mediated vesicle transport / COPII-coated ER to Golgi transport vesicle / RHOC GTPase cycle / Golgi organization / mannose binding / RHOG GTPase cycle / RHOA GTPase cycle / endoplasmic reticulum-Golgi intermediate compartment / RAC3 GTPase cycle / RAC2 GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / endoplasmic reticulum-Golgi intermediate compartment membrane / sarcomere / ER to Golgi transport vesicle membrane / unfolded protein binding / blood coagulation / protein transport / protein folding / collagen-containing extracellular matrix / Golgi membrane / calcium ion binding / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / extracellular exosome / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Nishio, M. / Kamiya, Y. / Mizushima, T. / Wakatsuki, S. / Sasakawa, H. / Yamamoto, K. / Uchiyama, S. / Noda, M. / McKay, A.R. / Fukui, K. ...Nishio, M. / Kamiya, Y. / Mizushima, T. / Wakatsuki, S. / Sasakawa, H. / Yamamoto, K. / Uchiyama, S. / Noda, M. / McKay, A.R. / Fukui, K. / Hauri, H.P. / Kato, K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Structural basis for the cooperative interplay between the two causative gene products of combined factor V and factor VIII deficiency. Authors: Nishio, M. / Kamiya, Y. / Mizushima, T. / Wakatsuki, S. / Sasakawa, H. / Yamamoto, K. / Uchiyama, S. / Noda, M. / McKay, A.R. / Fukui, K. / Hauri, H.P. / Kato, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a4u.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a4u.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 3a4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/3a4u ftp://data.pdbj.org/pub/pdb/validation_reports/a4/3a4u | HTTPS FTP |
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-Related structure data
Related structure data | 1r1zS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28039.068 Da / Num. of mol.: 1 / Fragment: Carbohydrate Recognition Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LMAN1, ERGIC53, F5F8D / Plasmid: pCold3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus / References: UniProt: P49257 | ||||
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#2: Protein | Mass: 16316.842 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCFD2, SDNSF / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus / References: UniProt: Q8NI22 | ||||
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.14 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% PEG 3350, 0.2M sodium tartrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2008 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→49.81 Å / Num. obs: 36530 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.84 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.188 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.84→1.94 Å / Redundancy: 7 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 6.1 / Num. unique all: 5229 / Rsym value: 0.188 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R1Z Resolution: 1.84→49.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.975 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.197 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→49.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.838→1.886 Å / Total num. of bins used: 20
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