+Open data
-Basic information
Entry | Database: PDB / ID: 4bq8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the RGMB-NEO1 complex form 3 | ||||||
Components |
| ||||||
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 / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of protein secretion / 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: 2.8 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4bq8.cif.gz | 163 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4bq8.ent.gz | 129.5 KB | Display | PDB format |
PDBx/mmJSON format | 4bq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/4bq8 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/4bq8 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24076.307 Da / Num. of mol.: 1 / Fragment: FN-TYPE III DOMAINS 5 AND 6, RESIDUES 883-1083 Source method: isolated from a genetically manipulated source Details: N-LINKED GLYCOSYLATION AT N940 / 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.: 1 / Fragment: ECTODOMAIN, 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.: 1 / Fragment: ECTODOMAIN, 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 |
#4: Sugar | ChemComp-NAG / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | N-ACETYL-D-GLUCOSAMIN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 68 % / Description: NONE |
---|---|
Crystal grow | pH: 4.5 Details: 0.1 M SODIUM ACETATE, PH 4.6, 0.18 M POTASSIUM ACETATE, 18 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9686 |
Detector | Type: DECTRIS PILATUS 6D / 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: 2.8→82.68 Å / Num. obs: 16184 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 91.14 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.9 / % possible all: 99.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.9345 / Cor.coef. Fo:Fc free: 0.9363 / SU R Cruickshank DPI: 0.414 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.419 / SU Rfree Blow DPI: 0.235 / SU Rfree Cruickshank DPI: 0.237 Details: THERE IS AN AUTOCATALYTIC CLEAVAGE SITE PRESENT IN RGMB (CHAIN B/C), WHICH IS LOCATED BETWEEN RESIDUES ASP168 AND PRO169.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.33 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.377 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.99 Å / Total num. of bins used: 8
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|