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- PDB-6v6q: Crystal Structure of Monophosphorylated FGF Receptor 2 isoform II... -

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Basic information

Entry
Database: PDB / ID: 6v6q
TitleCrystal Structure of Monophosphorylated FGF Receptor 2 isoform IIIb with PTR657
ComponentsFibroblast growth factor receptor 2
KeywordsTRANSFERASE / Fibroblast growth factor receptor 2
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 / lateral sprouting from an epithelium / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / 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 / lateral sprouting from an epithelium / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / lacrimal gland development / prostate gland morphogenesis / otic vesicle formation / regulation of smooth muscle cell differentiation / regulation of morphogenesis of a branching structure / orbitofrontal cortex development / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / embryonic organ morphogenesis / branching morphogenesis of a nerve / endochondral bone growth / morphogenesis of embryonic epithelium / bud elongation involved in lung branching / epidermis morphogenesis / positive regulation of epithelial cell proliferation involved in lung morphogenesis / reproductive structure development / limb bud formation / membranous septum morphogenesis / lung lobe morphogenesis / gland morphogenesis / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / embryonic digestive tract morphogenesis / mesenchymal cell differentiation / epithelial cell proliferation involved in salivary gland morphogenesis / branching involved in labyrinthine layer morphogenesis / mesenchymal cell proliferation involved in lung development / pyramidal neuron development / branching involved in prostate gland morphogenesis / FGFR2b ligand binding and activation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / regulation of osteoblast proliferation / branching involved in salivary gland morphogenesis / embryonic pattern specification / positive regulation of phospholipase activity / lung-associated mesenchyme development / outflow tract septum morphogenesis / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / mesodermal cell differentiation / bone morphogenesis / digestive tract development / skeletal system morphogenesis / odontogenesis / positive regulation of mesenchymal cell proliferation / ureteric bud development / inner ear morphogenesis / organ growth / hair follicle morphogenesis / Signaling by FGFR2 IIIa TM / ventricular cardiac muscle tissue morphogenesis / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of osteoblast differentiation / PI-3K cascade:FGFR2 / lung alveolus development / prostate epithelial cord elongation / midbrain development / bone mineralization / fibroblast growth factor binding / positive regulation of cell division / excitatory synapse / PI3K Cascade / positive regulation of Wnt signaling pathway / cell fate commitment / fibroblast growth factor receptor signaling pathway / epithelial to mesenchymal transition / negative regulation of keratinocyte proliferation / embryonic organ development / regulation of ERK1 and ERK2 cascade / SHC-mediated cascade:FGFR2 / positive regulation of cardiac muscle cell proliferation / cellular response to transforming growth factor beta stimulus / FRS-mediated FGFR2 signaling / cellular response to retinoic acid / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of cell cycle / Signaling by FGFR2 in disease / epithelial cell differentiation / axonogenesis / positive regulation of epithelial cell proliferation / post-embryonic development / animal organ morphogenesis / Negative regulation of FGFR2 signaling / lung development / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity
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. ...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. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / 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
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Fibroblast growth factor receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsLin, C.-C. / Wieteska, L. / Poncet-Montange, G. / Suen, K.M. / Arold, S.T. / Ahmed, Z. / Ladbury, J.E.
CitationJournal: Commun Biol / Year: 2023
Title: The combined action of the intracellular regions regulates FGFR2 kinase activity
Authors: Lin, C.C. / Wieteska, L. / Poncet-Montange, G. / Suen, K.M. / Arold, S.T. / Ahmed, Z. / Ladbury, J.E.
History
DepositionDec 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibroblast growth factor receptor 2
B: Fibroblast growth factor receptor 2
C: Fibroblast growth factor receptor 2
D: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,98212
Polymers185,8644
Non-polymers2,1188
Water2,252125
1
A: Fibroblast growth factor receptor 2
B: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9916
Polymers92,9322
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-41 kcal/mol
Surface area25660 Å2
MethodPISA
2
C: Fibroblast growth factor receptor 2
D: Fibroblast growth factor receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9916
Polymers92,9322
Non-polymers1,0594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-40 kcal/mol
Surface area25080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.970, 86.541, 254.162
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA467 - 76557 - 355
21THRTHRBB467 - 76557 - 355
12THRTHRAA467 - 76557 - 355
22THRTHRCC467 - 76557 - 355
13THRTHRAA467 - 76557 - 355
23THRTHRDD467 - 76557 - 355
14ASNASNBB467 - 76657 - 356
24ASNASNCC467 - 76657 - 356
15THRTHRBB467 - 76557 - 355
25THRTHRDD467 - 76557 - 355
16THRTHRCC467 - 76557 - 355
26THRTHRDD467 - 76557 - 355

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Fibroblast growth factor receptor 2 / FGFR-2 / K-sam / KGFR / Keratinocyte growth factor receptor


Mass: 46466.109 Da / Num. of mol.: 4
Mutation: Y467F,Y562F,Y576F,Y587F,Y589F,Y609F,Y617F,Y658F,Y734F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR2, BEK, KGFR, KSAM / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P21802, receptor protein-tyrosine kinase
#2: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 35.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 / Details: 160mM TMAO, 20% PEG 2000, 100mM Tris pH 8.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.46→127.08 Å / Num. obs: 50447 / % possible obs: 96.6 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.041 / Rrim(I) all: 0.112 / Net I/σ(I): 12.7 / Num. measured all: 338930
Reflection shellResolution: 2.46→2.59 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.088 / Num. measured all: 21237 / Num. unique obs: 5926 / CC1/2: 0.326 / Rpim(I) all: 0.564 / Rrim(I) all: 1.232 / Net I/σ(I) obs: 1.8 / % possible all: 80.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
MOSFLMdata reduction
Aimless3.3.21data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PSQ

2psq


Resolution: 2.46→82.06 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 23.081 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.504 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 2574 5.1 %RANDOM
Rwork0.2114 ---
obs0.2129 47559 95.93 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.33 Å2 / Biso mean: 67.138 Å2 / Biso min: 24.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: final / Resolution: 2.46→82.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9018 0 124 125 9267
Biso mean--83.82 49.06 -
Num. residues----1132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0139335
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178854
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.65112617
X-RAY DIFFRACTIONr_angle_other_deg1.1951.58120589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4951122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33822.5468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.633151715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2921560
X-RAY DIFFRACTIONr_chiral_restr0.0620.21192
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210135
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021881
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A90700.1
12B90700.1
21A86630.09
22C86630.09
31A86320.1
32D86320.1
41B87790.1
42C87790.1
51B85910.11
52D85910.11
61C86190.11
62D86190.11
LS refinement shellResolution: 2.46→2.524 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 140 -
Rwork0.366 2543 -
all-2683 -
obs--71.38 %
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)
13.8459-1.59390.01182.7548-1.20992.8658-0.514-0.3948-0.15910.51210.31330.0140.0958-0.06140.20070.34930.05570.16470.0623-0.02940.2116-10.481-23.81235.974
22.7435-1.0597-0.20362.1443-0.23371.28920.08140.09620.1854-0.09630.0255-0.0688-0.02740.0375-0.10680.0482-0.01470.04340.0135-0.01510.0919-6.897-6.0727.22
32.9802-0.8619-1.00472.66750.67182.84530.1901-0.04530.2977-0.01830.10640.0966-0.7021-0.3559-0.29660.38650.11080.22050.07160.08050.3712-31.1730.95625.012
44.04640.1929-2.05671.7697-0.60743.83950.138-0.26040.18970.4053-0.09530.02520.10350.1043-0.04270.57570.020.12460.2905-0.09560.2797-32.116.74656.646
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A466 - 765
2X-RAY DIFFRACTION2B467 - 766
3X-RAY DIFFRACTION3C467 - 766
4X-RAY DIFFRACTION4D467 - 765

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