[English] 日本語
Yorodumi
- PDB-3caf: Crystal Structure of hFGFR2 D2 Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3caf
TitleCrystal Structure of hFGFR2 D2 Domain
ComponentsFibroblast growth factor receptor 2
KeywordsTRANSFERASE / FGFR2 / D2 / Fibroblast Growth Factor / ATP-binding / Disease mutation / Ectodermal dysplasia / Glycoprotein / Heparin-binding / Immunoglobulin domain / Kinase / Lacrimo-auriculo-dento-digital syndrome / Membrane / Nucleotide-binding / Phosphoprotein / Receptor / Secreted / Transmembrane / Tyrosine-protein kinase
Function / homology
Function and homology information


Signaling by FGFR2 amplification mutants / Signaling by FGFR2 fusions / fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow cell / fibroblast growth factor receptor signaling pathway involved in hemopoiesis / fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development ...Signaling by FGFR2 amplification mutants / Signaling by FGFR2 fusions / fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow cell / fibroblast growth factor receptor signaling pathway involved in hemopoiesis / fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / lacrimal gland development / otic vesicle formation / prostate gland morphogenesis / regulation of smooth muscle cell differentiation / orbitofrontal cortex development / regulation of morphogenesis of a branching structure / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / branching morphogenesis of a nerve / embryonic organ morphogenesis / endochondral bone growth / morphogenesis of embryonic epithelium / epidermis morphogenesis / bud elongation involved in lung branching / positive regulation of epithelial cell proliferation involved in lung morphogenesis / pyramidal neuron development / membranous septum morphogenesis / reproductive structure development / limb bud formation / lung lobe morphogenesis / gland morphogenesis / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / embryonic digestive tract morphogenesis / epithelial cell proliferation involved in salivary gland morphogenesis / mesenchymal cell differentiation / branching involved in prostate gland morphogenesis / mesenchymal cell proliferation involved in lung development / branching involved in labyrinthine layer morphogenesis / FGFR2b ligand binding and activation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / regulation of osteoblast proliferation / Phospholipase C-mediated cascade; FGFR2 / fibroblast growth factor receptor activity / branching involved in salivary gland morphogenesis / embryonic pattern specification / outflow tract septum morphogenesis / positive regulation of phospholipase activity / lung-associated mesenchyme development / mesodermal cell differentiation / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / digestive tract development / bone morphogenesis / skeletal system morphogenesis / odontogenesis / positive regulation of mesenchymal cell proliferation / ureteric bud development / ventricular cardiac muscle tissue morphogenesis / regulation of osteoblast differentiation / Signaling by FGFR2 IIIa TM / inner ear morphogenesis / organ growth / midbrain development / hair follicle morphogenesis / lung alveolus development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / fibroblast growth factor binding / PI-3K cascade:FGFR2 / bone mineralization / prostate epithelial cord elongation / positive regulation of cell division / excitatory synapse / positive regulation of Wnt signaling pathway / PI3K Cascade / negative regulation of keratinocyte proliferation / epithelial to mesenchymal transition / fibroblast growth factor receptor signaling pathway / cell fate commitment / embryonic organ development / positive regulation of cell cycle / SHC-mediated cascade:FGFR2 / cellular response to retinoic acid / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR2 signaling / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to transforming growth factor beta stimulus / Signaling by FGFR2 in disease / epithelial cell differentiation / axonogenesis / regulation of ERK1 and ERK2 cascade / post-embryonic development / positive regulation of epithelial cell proliferation / Negative regulation of FGFR2 signaling / animal organ morphogenesis / lung development / bone development / receptor protein-tyrosine kinase / cell surface receptor protein tyrosine kinase signaling pathway / peptidyl-tyrosine phosphorylation
Similarity search - Function
Fibroblast growth factor receptor family / Immunoglobulin domain / 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 ...Fibroblast growth factor receptor family / Immunoglobulin domain / 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
Fibroblast growth factor receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsGuo, F. / Dakshinamurthy, R. / Kathir, K.M. / Thallapuranam, S.K.K. / Sakon, J.
CitationJournal: To be Published
Title: Crystal structure analysis of the hFGFR2 D2 domain
Authors: Guo, F. / Dakshinamurthy, R. / Kathir, K.M. / Thallapuranam, S.K.K. / Sakon, J.
History
DepositionFeb 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fibroblast growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)11,6081
Polymers11,6081
Non-polymers00
Water97354
1
A: Fibroblast growth factor receptor 2

A: Fibroblast growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)23,2172
Polymers23,2172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.500, 79.900, 37.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-26-

HOH

-
Components

#1: Protein Fibroblast growth factor receptor 2 / / FGFR-2 / Keratinocyte growth factor receptor 2 / CD332 antigen


Mass: 11608.258 Da / Num. of mol.: 1 / Fragment: Ig-like C2-type 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR2, BEK, KGFR, KSAM / Production host: Escherichia coli (E. coli)
References: UniProt: P21802, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20%(w/v) PEG3350, 0.1M (NH3)2SO4, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→16.76 Å / Num. obs: 9401 / % possible obs: 98.1 % / Redundancy: 3.39 % / Rmerge(I) obs: 0.048 / Χ2: 0.98 / Net I/σ(I): 14.4 / Scaling rejects: 242
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.96-2.032.220.3861.917477851.1284.9
2.03-2.112.810.3662.425419011.0296.8
2.11-2.213.460.3083.332989481.0699.8
2.21-2.323.630.243.93445943199.8
2.32-2.473.60.1974.933939350.9599.9
2.47-2.663.630.156.335249640.9100
2.66-2.923.660.0969.934439380.9199.7
2.92-3.343.640.05715.835359700.86100
3.34-4.23.610.03132.635809790.9899.8
4.2-16.763.390.02151.7358710381.1499.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.96 Å16.76 Å
Translation1.96 Å16.76 Å

-
Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→16.76 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.924 / SU B: 12.77 / SU ML: 0.163 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 416 4.9 %RANDOM
Rwork0.187 ---
obs0.191 8479 88.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.551 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.96→16.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 0 54 868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.021838
X-RAY DIFFRACTIONr_angle_refined_deg2.0821.9211134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.654599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.95823.41541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.78515145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.509156
X-RAY DIFFRACTIONr_chiral_restr0.1810.2115
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02644
X-RAY DIFFRACTIONr_nbd_refined0.2690.2338
X-RAY DIFFRACTIONr_nbtor_refined0.3310.2555
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.252
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.24
X-RAY DIFFRACTIONr_mcbond_it24.7642515
X-RAY DIFFRACTIONr_mcangle_it23.3743807
X-RAY DIFFRACTIONr_scbond_it2381
X-RAY DIFFRACTIONr_scangle_it87.4863327
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 6 -
Rwork0.276 169 -
all-175 -
obs--25.77 %
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)
124.122517.00045.708552.84575.44819.41460.5463-0.8995-1.22971.62430.0639-1.351.34930.2244-0.61020.04920.0022-0.0457-0.02590.07110.11655.2-5.96712.585
239.29630.3962-1.418219.5315-9.39044.55310.1252-3.66240.76642.6566-0.4747-0.4251-0.90620.49950.34960.3859-0.1245-0.00610.2168-0.04380.06083.8937.1717.948
332.24570086.689800-0.971-2.5009-0.51373.38231.62590.9132-1.9795-0.4485-0.65490.5482-0.0790.10780.1349-0.08170.17331.76214.99616.447
416.0395-1.5331-8.83783.1162-1.48746.70121.1358-1.09180.39490.9271-0.4074-0.3371-0.4373-0.0197-0.72850.1166-0.07010.00610.099-0.1890.20688.13327.13611.687
532.135231.7047-2.45559.5039-0.15920.3691.1663-2.6007-1.04412.6263-1.1568-1.7466-0.14440.4731-0.00960.07-0.0132-0.01130.1648-0.0976-0.132411.66917.99912.764
60.00030.04790.0287.69684.5032.63450.0696-0.5181-0.76771.0911-0.229-2.0155-0.20370.39090.15930.0374-0.0078-0.12630.02920.05460.180210.1280.43510.237
722.7035-7.4508021.2986019.9769-0.00830.4999-1.1964-1.1527-0.5154-0.49750.3630.36310.5237-0.1435-0.0454-0.0236-0.183-0.0399-0.23588.29212.2491.748
861.78327.92148.177124.57424.575613.06050.37492.5646-1.6802-0.52720.1192-0.25360.22520.9415-0.4941-0.1516-0.01150.005-0.0425-0.0139-0.16557.4715.082-2.876
915.70153.3712-3.194626.49867.453219.0498-0.33051.5601-0.3196-1.02760.6638-0.38990.3202-0.3711-0.3333-0.145-0.04830.04410.0299-0.05380.138216.5719.561-2.467
1013.69183.9409059.7734034.28490.5614-0.2768-0.93143.2053-2.3878-3.5828-1.2512.63971.82640.1919-0.0807-0.05390.0211-0.10840.284118.08714.6366.688
1129.64613.4503039.1544020.5093-0.5915-1.4585-0.55590.30940.665-5.6206-0.37862.4446-0.07360.066-0.0208-0.13080.3060.00210.385715.636.80812.798
122.01230.9790.565610.2495-9.24349.61740.2013-0.13590.62060.1423-0.2909-0.80520.17870.26290.0897-0.0976-0.0246-0.0127-0.0672-0.06470.175213.76823.1696.096
1312.13661.09880.34663.649-0.35758.2933-0.1362-0.10211.15470.16440.06120.0018-0.15620.00660.0751-0.2107-0.02260.0138-0.1411-0.0491-0.17145.07416.9243.768
1417.173212.34142.764779.654515.751619.62680.4040.1301-0.9522-0.9213-0.0364-0.20650.38370.2838-0.3675-0.23150.054-0.0769-0.1434-0.0143-0.02916.032-3.8124.821
156.43061.0479-4.558132.3671000.2251-0.3117-0.548-0.0416-0.3911.0258-0.2816-0.01640.166-0.1567-0.05180.0312-0.151-0.03970.00591.5986.916.818
1616.15269.7132-1.789119.1841-9.65488.80310.535-0.35591.58460.989-0.45542.2534-0.58780.1411-0.0797-0.0857-0.02480.1104-0.0695-0.10830.02734.39324.3598.179
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA150 - 1551 - 6
2X-RAY DIFFRACTION2AA156 - 1607 - 11
3X-RAY DIFFRACTION3AA161 - 16512 - 16
4X-RAY DIFFRACTION4AA166 - 17317 - 24
5X-RAY DIFFRACTION5AA174 - 17825 - 29
6X-RAY DIFFRACTION6AA179 - 18930 - 40
7X-RAY DIFFRACTION7AA190 - 19341 - 44
8X-RAY DIFFRACTION8AA194 - 19845 - 49
9X-RAY DIFFRACTION9AA199 - 20550 - 56
10X-RAY DIFFRACTION10AA206 - 21057 - 61
11X-RAY DIFFRACTION11AA211 - 21462 - 65
12X-RAY DIFFRACTION12AA215 - 22566 - 76
13X-RAY DIFFRACTION13AA226 - 23277 - 83
14X-RAY DIFFRACTION14AA233 - 23784 - 88
15X-RAY DIFFRACTION15AA238 - 24389 - 94
16X-RAY DIFFRACTION16AA244 - 24995 - 100

+
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