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- PDB-3hbw: Crystal Structure of Human Fibroblast Growth Factor Homologous Fa... -

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Basic information

Entry
Database: PDB / ID: 3hbw
TitleCrystal Structure of Human Fibroblast Growth Factor Homologous Factor 2A (FHF2A), also referred to as Fibroblast Growth Factor 13A (FGF13A)
ComponentsFibroblast growth factor 13
KeywordsHORMONE / beta-trefoil fold / Alternative splicing / Growth factor / Polymorphism
Function / homology
Function and homology information


establishment of neuroblast polarity / regulation of cardiac muscle cell action potential involved in regulation of contraction / negative regulation of collateral sprouting / positive regulation of voltage-gated sodium channel activity / branching morphogenesis of a nerve / inhibitory synapse assembly / negative regulation of microtubule depolymerization / sodium ion transport / beta-tubulin binding / Phase 0 - rapid depolarisation ...establishment of neuroblast polarity / regulation of cardiac muscle cell action potential involved in regulation of contraction / negative regulation of collateral sprouting / positive regulation of voltage-gated sodium channel activity / branching morphogenesis of a nerve / inhibitory synapse assembly / negative regulation of microtubule depolymerization / sodium ion transport / beta-tubulin binding / Phase 0 - rapid depolarisation / cerebral cortex cell migration / microtubule polymerization / intercalated disc / lateral plasma membrane / sodium channel regulator activity / learning / filopodium / protein localization to plasma membrane / hippocampus development / growth factor activity / neuron migration / sarcolemma / memory / MAPK cascade / cell-cell signaling / nervous system development / growth cone / microtubule binding / transmembrane transporter binding / microtubule / neuron projection / axon / dendrite / signal transduction / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMohammadi, M.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal structure of a fibroblast growth factor homologous factor (FHF) defines a conserved surface on FHFs for binding and modulation of voltage-gated sodium channels.
Authors: Goetz, R. / Dover, K. / Laezza, F. / Shtraizent, N. / Huang, X. / Tchetchik, D. / Eliseenkova, A.V. / Xu, C.F. / Neubert, T.A. / Ornitz, D.M. / Goldfarb, M. / Mohammadi, M.
History
DepositionMay 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fibroblast growth factor 13
B: Fibroblast growth factor 13


Theoretical massNumber of molelcules
Total (without water)43,6862
Polymers43,6862
Non-polymers00
Water2,342130
1
A: Fibroblast growth factor 13


Theoretical massNumber of molelcules
Total (without water)21,8431
Polymers21,8431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fibroblast growth factor 13


Theoretical massNumber of molelcules
Total (without water)21,8431
Polymers21,8431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.218, 57.998, 52.236
Angle α, β, γ (deg.)90.00, 93.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fibroblast growth factor 13 / FGF-13 / Fibroblast growth factor homologous factor 2 / FHF-2


Mass: 21842.871 Da / Num. of mol.: 2 / Fragment: UNP residues 53-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: FGF13, FHF2, fibroblast growth factor homologous factor 2 (FHF2)
Plasmid: pET30(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92913
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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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: 1.81 Å3/Da / Density % sol: 31.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PEG 4000, 0.2M ammonium sulfate, 0.1M HEPES-NaOH pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 26, 2006
RadiationMonochromator: KOHZU DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 23482 / Num. obs: 23482 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rsym value: 0.044 / Net I/σ(I): 64.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 13.7 / Num. unique all: 2119 / Rsym value: 0.202 / % possible all: 86.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q1U

1q1u


Resolution: 1.9→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 2272 -Random
Rwork0.2194 ---
all-23092 --
obs-23092 100 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.024 Å20 Å28.237 Å2
2--1.53 Å20 Å2
3----0.507 Å2
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2360 0 0 130 2490
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.9-1.910.225400.2727X-RAY DIFFRACTION463100
1.91-1.930.318360.262X-RAY DIFFRACTION463100
1.93-1.940.296400.2537X-RAY DIFFRACTION417100
1.94-1.960.296390.2424X-RAY DIFFRACTION466100
1.96-1.980.222380.2228X-RAY DIFFRACTION416100
1.98-1.990.304430.2262X-RAY DIFFRACTION498100

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