[English] 日本語
Yorodumi
- PDB-2v9r: First and second Ig domains from human Robo1 (Form 2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2v9r
TitleFirst and second Ig domains from human Robo1 (Form 2)
ComponentsROUNDABOUT HOMOLOG 1
KeywordsRECEPTOR / PROTO-ONCOGENE / DIFFERENTIATION / PHOSPHORYLATION / DISEASE MUTATION / NEURONAL DEVELOPMENT / IMMUNOGLOBULIN DOMAIN / CHEMOTAXIS / NEUROGENESIS / GLYCOPROTEIN / TRANSMEMBRANE / ROBO1 / MEMBRANE / IG DOMAIN / ROUNDABOUT / DEVELOPMENTAL PROTEIN
Function / homology
Function and homology information


chemorepulsion involved in postnatal olfactory bulb interneuron migration / negative regulation of negative chemotaxis / Regulation of cortical dendrite branching / negative regulation of mammary gland epithelial cell proliferation / LRR domain binding / negative regulation of chemokine-mediated signaling pathway / heart induction / axon guidance receptor activity / Netrin-1 signaling / positive regulation of vascular endothelial growth factor signaling pathway ...chemorepulsion involved in postnatal olfactory bulb interneuron migration / negative regulation of negative chemotaxis / Regulation of cortical dendrite branching / negative regulation of mammary gland epithelial cell proliferation / LRR domain binding / negative regulation of chemokine-mediated signaling pathway / heart induction / axon guidance receptor activity / Netrin-1 signaling / positive regulation of vascular endothelial growth factor signaling pathway / Regulation of commissural axon pathfinding by SLIT and ROBO / Role of ABL in ROBO-SLIT signaling / SLIT2:ROBO1 increases RHOA activity / Roundabout signaling pathway / Inactivation of CDC42 and RAC1 / outflow tract septum morphogenesis / endocardial cushion formation / Signaling by ROBO receptors / pulmonary valve morphogenesis / positive regulation of vascular endothelial growth factor receptor signaling pathway / cell migration involved in sprouting angiogenesis / Activation of RAC1 / aortic valve morphogenesis / axon midline choice point recognition / aorta development / positive regulation of axonogenesis / positive regulation of Rho protein signal transduction / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / homophilic cell adhesion via plasma membrane adhesion molecules / endoplasmic reticulum-Golgi intermediate compartment membrane / negative regulation of cell migration / positive regulation of MAP kinase activity / : / Regulation of expression of SLITs and ROBOs / nervous system development / cell adhesion / neuron projection / axon / negative regulation of gene expression / positive regulation of gene expression / cell surface / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Roundabout homologue 1 / : / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type ...Roundabout homologue 1 / : / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Roundabout homolog 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMorlot, C. / Cusack, S. / McCarthy, A.A.
Citation
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Cloning, Expression, Crystallization and Preliminary X-Ray Analysis of the First Two Ig Domains from Human Roundabout 1 (Robo1).
Authors: Morlot, C. / Hemrika, W. / Romijn, R.A. / Gros, P. / Cusack, S. / Mccarthy, A.A.
History
DepositionAug 25, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ROUNDABOUT HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7803
Polymers23,5881
Non-polymers1922
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.460, 108.100, 25.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2041-

HOH

-
Components

#1: Protein ROUNDABOUT HOMOLOG 1 / H-ROBO-1 / DELETED IN U TWENTY TWENTY / ROBO1


Mass: 23587.717 Da / Num. of mol.: 1 / Fragment: IG1-2M, RESIDUES 61-266 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293-EBNA1 / Production host: HOMO SAPIENS (human) / References: UniProt: Q9Y6N7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 160 TO ASP
Has protein modificationY
Sequence detailsA N160D MUTATION WAS MADE TO PREVENT POTENTIAL GLYCOSYLATION

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 5.6 / Details: 12% PEG 6000, 0.1M LISO4, 0.1M NA CITRATE, pH 5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 3, 2006 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 54927 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.6
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 7 / % possible all: 94.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V9Q

2v9q


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.837 / SU B: 15.071 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS IS A SECOND CRYSTAL FORM OF THE SUBMISSION ABOVE, ROBO1 IG1-2. ALTHOUGH IT DIFFRACTED TO A HIGHER RESOLUTION THE R AND RFREE ARE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS IS A SECOND CRYSTAL FORM OF THE SUBMISSION ABOVE, ROBO1 IG1-2. ALTHOUGH IT DIFFRACTED TO A HIGHER RESOLUTION THE R AND RFREE ARE LARGER THAN EXPECTED FOR THIS RESOLUTION. THIS IS PROBABLY DUE TO THE PRESENCE OF A WEAK SUPER LATTICE THAT WAS OBSERVED IN THE DIFFRACTION PATTERN.
RfactorNum. reflection% reflectionSelection details
Rfree0.335 751 5.1 %RANDOM
Rwork0.258 ---
obs0.261 14074 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.74 Å2
Baniso -1Baniso -2Baniso -3
1-2.87 Å20 Å20 Å2
2---2.54 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 10 53 1594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221606
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.9862184
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2915204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33723.05672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.60515280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6741517
X-RAY DIFFRACTIONr_chiral_restr0.1170.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021227
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.2640
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21042
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3540.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7871.51032
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19921631
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9043642
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8114.5550
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.466 49
Rwork0.317 1034
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1748-0.1051-0.55432.36810.38311.8198-0.0549-0.1473-0.0594-0.0032-0.00840.1012-0.0914-0.12380.06340.00370.0916-0.00010.0664-0.0016-0.094432.53765.717-5.053
25.43225.8593-2.77056.5921-2.54082.14910.28240.15451.2760.11090.2811.0686-0.1544-0.1327-0.56330.1287-0.02780.04560.02570.08050.35352.65538.4418.792
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A64 - 165
2X-RAY DIFFRACTION2A166 - 260

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more