[English] 日本語
Yorodumi
- PDB-3cu1: Crystal Structure of 2:2:2 FGFR2D2:FGF1:SOS complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cu1
TitleCrystal Structure of 2:2:2 FGFR2D2:FGF1:SOS complex
Components
  • Fibroblast growth factor receptor 2
  • Heparin-binding growth factor 1
KeywordsTransferase/Hormone / Fibroblast growth factor 1 / Fibroblast growth factor receptor 2 / D2 domain / sucrose octa sulfate / Alternative splicing / ATP-binding / Disease mutation / Ectodermal dysplasia / Glycoprotein / Heparin-binding / Immunoglobulin domain / Kinase / Lacrimo-auriculo-dento-digital syndrome / Membrane / Nucleotide-binding / Phosphoprotein / Polymorphism / Secreted / Transferase / Transmembrane / Tyrosine-protein kinase / Acetylation / Angiogenesis / Developmental protein / Differentiation / Mitogen / Transferase-Hormone COMPLEX
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 / mesonephric epithelium development / branch elongation involved in ureteric bud branching / positive regulation of epithelial cell proliferation involved in lung morphogenesis / pyramidal neuron development / regulation of endothelial tube morphogenesis / membranous septum morphogenesis / reproductive structure development / limb bud formation / lung lobe morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / 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 / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / mesenchymal cell proliferation involved in lung development / Phospholipase C-mediated cascade; FGFR3 / branching involved in labyrinthine layer morphogenesis / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / regulation of osteoblast proliferation / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / fibroblast growth factor receptor activity / branching involved in salivary gland morphogenesis / Phospholipase C-mediated cascade; FGFR4 / embryonic pattern specification / outflow tract septum morphogenesis / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / lung-associated mesenchyme development / mesodermal cell differentiation / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / digestive tract development / positive regulation of hepatocyte proliferation / bone morphogenesis / S100 protein binding / skeletal system morphogenesis / odontogenesis / positive regulation of intracellular signal transduction / positive regulation of mesenchymal cell proliferation / ureteric bud development / ventricular cardiac muscle tissue morphogenesis / regulation of osteoblast differentiation / Signaling by FGFR2 IIIa TM / organ growth / inner ear morphogenesis / midbrain development / hair follicle morphogenesis / PI-3K cascade:FGFR3 / lung alveolus development / fibroblast growth factor binding / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR2 / bone mineralization / PI-3K cascade:FGFR4 / prostate epithelial cord elongation / PI-3K cascade:FGFR1 / positive regulation of cell division / excitatory synapse / positive regulation of Wnt signaling pathway / PI3K Cascade
Similarity search - Function
HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Fibroblast growth factor receptor family / Cytokine IL1/FGF / Immunoglobulin domain / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil ...HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Fibroblast growth factor receptor family / Cytokine IL1/FGF / Immunoglobulin domain / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / 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
sucrose octasulfate / Fibroblast growth factor 1 / Fibroblast growth factor receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsGuo, F. / Dakshinamurthy, R. / Thallapuranam, S.K.K. / Sakon, J.
CitationJournal: To be Published
Title: Crystal structure of 2:2:2 FGFR2D2:FGF1:SOS complex
Authors: Guo, F. / Dakshinamurthy, R. / Thallapuranam, S.K.K. / Sakon, J.
History
DepositionApr 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fibroblast growth factor receptor 2
B: Heparin-binding growth factor 1
C: Fibroblast growth factor receptor 2
D: Heparin-binding growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0686
Polymers53,1024
Non-polymers1,9662
Water6,179343
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.929, 110.375, 74.699
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
32B
42D
52B
62D
72B
82D
92B
102D
112B
122D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNVAL2AA150 - 2491 - 100
211ASNVAL2CC150 - 2491 - 100
112LYSPRO6BB10 - 114 - 5
212LYSPRO6DD10 - 114 - 5
322LYSSER2BB12 - 476 - 41
422LYSSER2DD12 - 476 - 41
532ALAGLY6BB48 - 5242 - 46
632ALAGLY6DD48 - 5242 - 46
742GLUGLU2BB53 - 9047 - 84
842GLUGLU2DD53 - 9047 - 84
952GLUHIS3BB91 - 9385 - 87
1052GLUHIS3DD91 - 9385 - 87
1162TYRVAL2BB94 - 13788 - 131
1262TYRVAL2DD94 - 13788 - 131

NCS ensembles :
ID
1
2

-
Components

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


Mass: 11608.258 Da / Num. of mol.: 2 / Fragment: Ig-like C2-type 2 domain, UNP residues 150-249
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: Protein Heparin-binding growth factor 1 / HBGF-1 / Acidic fibroblast growth factor / aFGF / Beta-endothelial cell growth factor / ECGF- beta


Mass: 14942.903 Da / Num. of mol.: 2 / Fragment: UNP residues 22-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Production host: Escherichia coli (E. coli) / References: UniProt: P05230
#3: Polysaccharide 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose / sucrose octasulfate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 982.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose octasulfate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_1*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf1SO33SO34SO36SO3]{[(2+1)][a-D-Glcp2SO33SO34SO36SO3]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% PEG3350, 4% Tacsimate, pH 7.0, vapor diffusion, hanging drop, temperature 298.0K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorDetector: CCD / Date: Jul 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. obs: 21046 / % possible obs: 93.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 20.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.6-2.692.90.28167.9
2.69-2.83.20.29582.2
2.8-2.933.70.26195.1
2.93-3.084.10.20899.3
3.08-3.284.30.16199.9
3.28-3.534.30.10299.6
3.53-3.884.10.07199.2
3.88-4.4540.05599
4.45-5.63.90.04898.5
5.6-1003.60.03891.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å44.39 Å
Translation4 Å44.39 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→42.95 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.89 / SU B: 22.26 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R: 0.641 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2768 1044 5.2 %RANDOM
Rwork0.18034 ---
obs0.18522 19219 89.99 %-
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: 16.979 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2---1.49 Å20 Å2
3---1.07 Å2
Refinement stepCycle: LAST / Resolution: 2.6→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 110 343 4183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0530.0213939
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.1361.985355
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3685455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13323.81189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75215677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.921525
X-RAY DIFFRACTIONr_chiral_restr0.2810.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022925
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3620.22057
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3570.22612
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3030.2283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3190.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.97722401
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53433687
X-RAY DIFFRACTIONr_scbond_it1.15821833
X-RAY DIFFRACTIONr_scangle_it1.98131668
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A400tight positional0.080.05
22B484tight positional0.070.05
11A418medium positional0.610.5
22B476medium positional0.730.5
22B62loose positional1.195
11A400tight thermal0.190.5
22B484tight thermal0.180.5
11A418medium thermal0.962
22B476medium thermal0.692
22B62loose thermal2.9610
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 28 -
Rwork0.238 580 -
obs--37.12 %

+
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