[English] 日本語
Yorodumi
- PDB-3wih: Crystal structure of the third fibronectin domain (Fn3) of human ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wih
TitleCrystal structure of the third fibronectin domain (Fn3) of human ROBO1 in complex with the Fab fragment of murine monoclonal antibody B2212A.
Components
  • Roundabout homolog 1
  • anti-human ROBO1 antibody B2212A Fab heavy chain
  • anti-human ROBO1 antibody B2212A Fab light chain
KeywordsIMMUNE SYSTEM / fibronectin type-III domain / hepatocellular carcinoma antigen / angiogenesis
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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsNakayama, T. / Mizohata, E. / Yamashita, T. / Nagatoishi, M. / Iwanari, H. / Mochizuki, Y. / Kado, Y. / Yokota, Y. / Sato, R. / Tsumoto, K. ...Nakayama, T. / Mizohata, E. / Yamashita, T. / Nagatoishi, M. / Iwanari, H. / Mochizuki, Y. / Kado, Y. / Yokota, Y. / Sato, R. / Tsumoto, K. / Fujitani, H. / Kodama, T. / Hamakubo, T. / Inoue, T.
CitationJournal: Protein Sci. / Year: 2015
Title: Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses
Authors: Nakayama, T. / Mizohata, E. / Yamashita, T. / Nagatoishi, S. / Nakakido, M. / Iwanari, H. / Mochizuki, Y. / Kado, Y. / Yokota, Y. / Satoh, R. / Tsumoto, K. / Fujitani, H. / Kodama, T. / Hamakubo, T. / Inoue, T.
History
DepositionSep 12, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Roundabout homolog 1
L: anti-human ROBO1 antibody B2212A Fab light chain
H: anti-human ROBO1 antibody B2212A Fab heavy chain
B: Roundabout homolog 1
M: anti-human ROBO1 antibody B2212A Fab light chain
I: anti-human ROBO1 antibody B2212A Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,5048
Polymers115,3206
Non-polymers1842
Water19,6901093
1
A: Roundabout homolog 1
L: anti-human ROBO1 antibody B2212A Fab light chain
H: anti-human ROBO1 antibody B2212A Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7524
Polymers57,6603
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-31 kcal/mol
Surface area23570 Å2
MethodPISA
2
B: Roundabout homolog 1
M: anti-human ROBO1 antibody B2212A Fab light chain
I: anti-human ROBO1 antibody B2212A Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7524
Polymers57,6603
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-30 kcal/mol
Surface area23450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.474, 102.601, 97.236
Angle α, β, γ (deg.)90.00, 127.57, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-643-

HOH

-
Components

#1: Protein Roundabout homolog 1 / Deleted in U twenty twenty / H-Robo-1


Mass: 10356.519 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUTT1, ROBO1, Roundabout homolog 1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6N7
#2: Antibody anti-human ROBO1 antibody B2212A Fab light chain


Mass: 23570.998 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody anti-human ROBO1 antibody B2212A Fab heavy chain


Mass: 23732.439 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1093 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR CHAIN L(M) AND CHAIN H(I) DOES NOT CURRENTLY EXIST. THESE ...A SEQUENCE DATABASE REFERENCE FOR CHAIN L(M) AND CHAIN H(I) DOES NOT CURRENTLY EXIST. THESE PROTEINS ARE THE ANTIBODY AGAINST CHAIN A(B).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 25.5%(w/v) PEG4000, 0.085M Na citrate tribasic dehydrate, 0.17M ammonium acetate, 15%(v/v) glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 128266 / % possible obs: 94.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.7-1.762.30.215191.9
1.76-1.832.40.168192.4
1.83-1.912.60.128192.3
1.91-2.022.80.09195
2.02-2.1430.072195.9
2.14-2.3130.059195.7
2.31-2.5430.049194.4
2.54-2.9130.04194.5
2.91-3.663.40.028197.1
3.66-503.40.024194.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIX1.8.4_1496refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X5H for CHAIN A(B), 3OZ9 for CHAIN L(M), H(I)

1x5h

3oz9


Resolution: 1.701→14.906 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.19 / σ(F): 0.09 / Phase error: 25.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 6422 5.02 %
Rwork0.1892 --
obs0.1916 127984 94.4 %
all-128266 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 10.7763 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.701→14.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7992 0 12 1093 9097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038283
X-RAY DIFFRACTIONf_angle_d0.77411277
X-RAY DIFFRACTIONf_dihedral_angle_d11.9172971
X-RAY DIFFRACTIONf_chiral_restr0.031281
X-RAY DIFFRACTIONf_plane_restr0.0041434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.701-1.72030.31012130.28153852X-RAY DIFFRACTION91
1.7203-1.74050.33012010.27623929X-RAY DIFFRACTION92
1.7405-1.76170.30582000.26053968X-RAY DIFFRACTION92
1.7617-1.7840.28272240.2443957X-RAY DIFFRACTION93
1.784-1.80740.25532050.22273936X-RAY DIFFRACTION92
1.8074-1.83220.27792380.2263964X-RAY DIFFRACTION92
1.8322-1.85830.27062110.22323930X-RAY DIFFRACTION91
1.8583-1.8860.25541910.21753892X-RAY DIFFRACTION92
1.886-1.91540.24421810.20644009X-RAY DIFFRACTION93
1.9154-1.94670.25962180.18464065X-RAY DIFFRACTION94
1.9467-1.98020.24022270.18074035X-RAY DIFFRACTION95
1.9802-2.01610.23152320.18244105X-RAY DIFFRACTION96
2.0161-2.05480.23712450.19074059X-RAY DIFFRACTION96
2.0548-2.09670.24722010.18934103X-RAY DIFFRACTION96
2.0967-2.14210.22972200.1834098X-RAY DIFFRACTION96
2.1421-2.19180.272020.18644128X-RAY DIFFRACTION96
2.1918-2.24640.24412100.19164132X-RAY DIFFRACTION96
2.2464-2.30690.24292160.19414105X-RAY DIFFRACTION95
2.3069-2.37460.24492230.19314046X-RAY DIFFRACTION94
2.3746-2.45090.28472270.19563966X-RAY DIFFRACTION95
2.4509-2.53810.26012120.20384093X-RAY DIFFRACTION95
2.5381-2.63920.24372150.20574047X-RAY DIFFRACTION94
2.6392-2.75860.25481910.20454066X-RAY DIFFRACTION95
2.7586-2.9030.2761820.20494105X-RAY DIFFRACTION95
2.903-3.08340.25222060.18994161X-RAY DIFFRACTION96
3.0834-3.3190.21942500.18094161X-RAY DIFFRACTION97
3.319-3.64860.20712090.16664240X-RAY DIFFRACTION98
3.6486-4.16640.20122260.16124183X-RAY DIFFRACTION97
4.1664-5.21170.19262130.15694193X-RAY DIFFRACTION96
5.2117-14.90670.23132330.19994034X-RAY DIFFRACTION92
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)
14.05520.0473-0.27081.45050.25296.30320.1469-0.3237-0.01290.0454-0.1832-0.12760.09630.21620.03630.05950.08030.00070.5530.05410.014529.226-7.369634.5687
20.6859-0.27720.20640.4884-0.29781.31690.04330.1367-0.2271-0.11310.00640.06540.24820.1567-0.04970.13880.0214-0.00230.3579-0.06690.161713.184-5.1964-8.7831
30.9431-0.40280.44930.4422-0.35751.2281-0.04840.10940.00870.0152-0.063-0.01210.00890.29780.11130.0440.00140.00120.39820.00090.066219.08168.906-0.4088
46.2085-0.1593-1.04990.87050.11424.06460.05230.13140.1456-0.0357-0.17090.0731-0.0211-0.37620.11860.04190.06760.00770.52270.05820.0441-40.898756.5844-19.2603
51.458-0.37310.05560.4715-0.18730.6566-0.03260.21450.28250.0295-0.0027-0.1362-0.19190.08440.03530.1667-0.0647-0.00810.35980.04030.14495.29554.4991-15.0174
61.5242-0.44870.34460.4653-0.29650.72130.10930.3299-0.0325-0.0158-0.06490.0144-0.03240.0259-0.04440.0690.0018-0.00470.4058-0.00030.025-4.802940.4552-18.7497
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:99 OR RESID 201:256 ) )A4 - 99
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:99 OR RESID 201:256 ) )A201 - 256
3X-RAY DIFFRACTION2( CHAIN L AND ( RESID 1:213 OR RESID 301:498 ) )L1 - 213
4X-RAY DIFFRACTION2( CHAIN L AND ( RESID 1:213 OR RESID 301:498 ) )L301 - 498
5X-RAY DIFFRACTION3( CHAIN H AND ( RESID 1:219 OR RESID 301:301 OR RESID 401:669 ) )H1 - 219
6X-RAY DIFFRACTION3( CHAIN H AND ( RESID 1:219 OR RESID 301:301 OR RESID 401:669 ) )H301
7X-RAY DIFFRACTION3( CHAIN H AND ( RESID 1:219 OR RESID 301:301 OR RESID 401:669 ) )H401 - 669
8X-RAY DIFFRACTION4( CHAIN B AND ( RESID 4:99 OR RESID 201:270 ) )B4 - 99
9X-RAY DIFFRACTION4( CHAIN B AND ( RESID 4:99 OR RESID 201:270 ) )B201 - 270
10X-RAY DIFFRACTION5( CHAIN M AND ( RESID 1:213 OR RESID 301:515 ) )M1 - 213
11X-RAY DIFFRACTION5( CHAIN M AND ( RESID 1:213 OR RESID 301:515 ) )M301 - 515
12X-RAY DIFFRACTION6( CHAIN I AND ( RESID 1:219 OR RESID 1001:1001 OR RESID 1101:1386 ) )I1 - 219
13X-RAY DIFFRACTION6( CHAIN I AND ( RESID 1:219 OR RESID 1001:1001 OR RESID 1101:1386 ) )I1001
14X-RAY DIFFRACTION6( CHAIN I AND ( RESID 1:219 OR RESID 1001:1001 OR RESID 1101:1386 ) )I1101 - 1386

+
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