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Yorodumi- PDB-4ygb: Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-free form -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ygb | ||||||||||||
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Title | Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-free form | ||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / BETA-SANDWICH / EF-HAND / CARGO RECEPTOR / CALCIUM BINDING / ER / ERGIC | ||||||||||||
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: 1.6 Å | ||||||||||||
Authors | Satoh, T. / Nishio, M. / Yagi-Utsumi, M. / Suzuki, K. / Anzai, T. / Mizushima, T. / Kamiya, Y. / Kato, K. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2020 Title: Crystallographic snapshots of the EF-hand protein MCFD2 complexed with the intracellular lectin ERGIC-53 involved in glycoprotein transport. Authors: Satoh, T. / Nishio, M. / Suzuki, K. / Yagi-Utsumi, M. / Kamiya, Y. / Mizushima, T. / Kato, K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ygb.cif.gz | 127.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ygb.ent.gz | 94.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ygb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/4ygb ftp://data.pdbj.org/pub/pdb/validation_reports/yg/4ygb | HTTPS FTP |
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-Related structure data
Related structure data | 4ygcC 4ygdC 4ygeC 3a4uS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 27154.230 Da / Num. of mol.: 2 / Fragment: UNP residues 31-269 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LMAN1, ERGIC53, F5F8D / Plasmid: PCOLD-III / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3) / References: UniProt: P49257 #2: Protein | Mass: 12056.186 Da / Num. of mol.: 2 / Fragment: UNP residues 67-146 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCFD2, SDNSF / Plasmid: PET-16B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3) / References: UniProt: Q8NI22 #3: Chemical | #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.2 M sodium malonate, 0.5% (v/v) Jeffamine ED-2001, 50 mM Tris-HCl |
-Data collection
Diffraction | Mean temperature: 95 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: Nov 22, 2013 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 88266 / Num. obs: 87258 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 19.58 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 39.2 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A4U Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.357 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.075 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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