+Open data
-Basic information
Entry | Database: PDB / ID: 4bq7 | ||||||
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Title | Crystal structure of the RGMB-Neo1 complex form 2 | ||||||
Components |
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Keywords | CELL ADHESION | ||||||
Function / homology | Function and homology information negative regulation of axon regeneration / Netrin-1 signaling / co-receptor binding / BMP receptor binding / regulation of axon regeneration / myoblast fusion / plasma membrane protein complex / positive regulation of BMP signaling pathway / intracellular vesicle / protein secretion ...negative regulation of axon regeneration / Netrin-1 signaling / co-receptor binding / BMP receptor binding / regulation of axon regeneration / myoblast fusion / plasma membrane protein complex / positive regulation of BMP signaling pathway / intracellular vesicle / protein secretion / negative regulation of protein secretion / endoplasmic reticulum-Golgi intermediate compartment / BMP signaling pathway / coreceptor activity / side of membrane / axonal growth cone / axon guidance / neuron migration / cell-cell adhesion / multicellular organismal-level iron ion homeostasis / signaling receptor activity / growth cone / intracellular iron ion homeostasis / cell adhesion / cadherin binding / membrane raft / neuronal cell body / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / Golgi apparatus / cell surface / signal transduction / nucleoplasm / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.601 Å | ||||||
Authors | Bell, C.H. / Healey, E. / van Erp, S. / Bishop, B. / Tang, C. / Gilbert, R.J.C. / Aricescu, A.R. / Pasterkamp, R.J. / Siebold, C. | ||||||
Citation | Journal: Science / Year: 2013 Title: Structure of the Repulsive Guidance Molecule (Rgm)-Neogenin Signaling Hub Authors: Bell, C.H. / Healey, E. / Van Erp, S. / Bishop, B. / Tang, C. / Gilbert, R.J.C. / Aricescu, A.R. / Pasterkamp, R.J. / Siebold, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bq7.cif.gz | 305.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bq7.ent.gz | 257.9 KB | Display | PDB format |
PDBx/mmJSON format | 4bq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/4bq7 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/4bq7 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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-Components
#1: Protein | Mass: 29221.842 Da / Num. of mol.: 2 / Fragment: FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1133 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P97798 #2: Protein | Mass: 13318.698 Da / Num. of mol.: 2 / Fragment: RESIDUES 50-168 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q6NW40 #3: Protein | Mass: 27945.352 Da / Num. of mol.: 2 / Fragment: RESIDUES 169-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q6NW40 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 65 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.1 M TRIS-HCL, PH 8.5, 0.2 M LITHIUM SULPHATE, 25 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9686 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 6.6→50 Å / Num. obs: 2508 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 121.5 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 6.6→6.8 Å / Redundancy: 5 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.3 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 6.601→84.779 Å / SU ML: 0.99 / σ(F): 1.36 / Phase error: 27.17 / Stereochemistry target values: ML Details: THERE IS AN AUTOCATALYTIC CLEAVAGE SITE PRESENT IN RGMB ( CHAINS C AND D), WHICH IS LOCATED BETWEEN RESIDUES ASP168 AND PRO169. IN ADDITION, NEO1 RESIDUES R967 AND R968 IN ( CHAIN A AND B) ...Details: THERE IS AN AUTOCATALYTIC CLEAVAGE SITE PRESENT IN RGMB ( CHAINS C AND D), WHICH IS LOCATED BETWEEN RESIDUES ASP168 AND PRO169. IN ADDITION, NEO1 RESIDUES R967 AND R968 IN ( CHAIN A AND B) WERE BUILT AS ALANINES.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 6.601→84.779 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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