[English] 日本語
Yorodumi
- PDB-3grw: FGFR3 in complex with a Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3grw
TitleFGFR3 in complex with a Fab
Components
  • Fab heavy chain
  • Fab light chain
  • Fibroblast growth factor receptor 3
KeywordsTRANSFERASE/IMMUNE SYSTEM / FGFR3 / Fab / protein-protein complex / receptor tyrosine kinase / ATP-binding / Immunoglobulin domain / Kinase / Membrane / Nucleotide-binding / Receptor / Transferase / Transmembrane / Tyrosine-protein kinase / TRANSFERASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


fibroblast growth factor receptor activity / receptor protein-tyrosine kinase / membrane => GO:0016020 / positive regulation of cell population proliferation / ATP binding / plasma membrane
Similarity search - Function
: / : / Fibroblast growth factor receptor family / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. ...: / : / Fibroblast growth factor receptor family / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Receptor protein-tyrosine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWiesmann, C.
CitationJournal: J.Clin.Invest. / Year: 2009
Title: Antibody-based targeting of FGFR3 in bladder carcinoma and t(4;14)-positive multiple myeloma in mice.
Authors: Qing, J. / Du, X. / Chen, Y. / Chan, P. / Li, H. / Wu, P. / Marsters, S. / Stawicki, S. / Tien, J. / Totpal, K. / Ross, S. / Stinson, S. / Dornan, D. / French, D. / Wang, Q.R. / Stephan, J.P. ...Authors: Qing, J. / Du, X. / Chen, Y. / Chan, P. / Li, H. / Wu, P. / Marsters, S. / Stawicki, S. / Tien, J. / Totpal, K. / Ross, S. / Stinson, S. / Dornan, D. / French, D. / Wang, Q.R. / Stephan, J.P. / Wu, Y. / Wiesmann, C. / Ashkenazi, A.
History
DepositionMar 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fibroblast growth factor receptor 3
L: Fab light chain
H: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4365
Polymers75,1193
Non-polymers3172
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-38 kcal/mol
Surface area30440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.049, 99.329, 143.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Antibody , 2 types, 2 molecules LH

#2: Antibody Fab light chain


Mass: 23287.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Protein selected by phage display / Production host: Escherichia coli (E. coli)
#3: Antibody Fab heavy chain


Mass: 24992.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Protein selected by phage display / Production host: Escherichia coli (E. coli)

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Fibroblast growth factor receptor 3


Mass: 26838.121 Da / Num. of mol.: 1 / Fragment: domains 2 and 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8NI16
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 2 types, 275 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 6.5
Details: 40% MPD, 5% PEG 8000, 0.1M Sodium Cacodylate, pH 6.5, EVAPORATION, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2007 / Details: Mirror
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 49851 / Num. obs: 49786 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.18 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.29 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22846 2499 5.1 %RANDOM
Rwork0.18933 ---
obs0.19134 46714 99.94 %-
all-46744 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.486 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å20 Å2
2---0.41 Å20 Å2
3---2.31 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4981 0 19 274 5274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225127
X-RAY DIFFRACTIONr_bond_other_d0.0070.023442
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.9566986
X-RAY DIFFRACTIONr_angle_other_deg0.9213.0038383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7955647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08523.768207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76615811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6321528
X-RAY DIFFRACTIONr_chiral_restr0.0860.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025709
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021027
X-RAY DIFFRACTIONr_nbd_refined0.1860.2718
X-RAY DIFFRACTIONr_nbd_other0.2060.23250
X-RAY DIFFRACTIONr_nbtor_refined0.170.22318
X-RAY DIFFRACTIONr_nbtor_other0.0840.22829
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3062.54141
X-RAY DIFFRACTIONr_mcbond_other0.6332.51310
X-RAY DIFFRACTIONr_mcangle_it4.75255244
X-RAY DIFFRACTIONr_scbond_it4.1062.52251
X-RAY DIFFRACTIONr_scangle_it5.37851742
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.143 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.336 132 -
Rwork0.243 2715 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 28.8768 Å / Origin y: 2.9451 Å / Origin z: -26.265 Å
111213212223313233
T-0.0303 Å20.0189 Å20.0329 Å2--0.0295 Å20.0075 Å2---0.0179 Å2
L0.51 °20.2441 °2-0.0799 °2-0.2455 °20.0152 °2--0.0789 °2
S0.0267 Å °-0.0301 Å °-0.0226 Å °0.0277 Å °-0.0064 Å °-0.0028 Å °0.0126 Å °0.0148 Å °-0.0203 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L215 - 311
2X-RAY DIFFRACTION1H223 - 339
3X-RAY DIFFRACTION1A2 - 410
4X-RAY DIFFRACTION1H222
5X-RAY DIFFRACTION1A1
6X-RAY DIFFRACTION1L1 - 214
7X-RAY DIFFRACTION1H1 - 216
8X-RAY DIFFRACTION1A150 - 355

+
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://pdbjlvh1.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