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- PDB-6ktr: Crystal structure of fibroblast growth factor 19 in complex with Fab -

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Basic information

Entry
Database: PDB / ID: 6ktr
TitleCrystal structure of fibroblast growth factor 19 in complex with Fab
Components
  • Fibroblast growth factor 19
  • G1A8-Fab-HC
  • G1A8-Fab-LC
KeywordsIMMUNE SYSTEM/PROTEIN BINDING / complex / growth factor / antibody / CELL CYCLE / IMMUNE SYSTEM-PROTEIN BINDING complex
Function / homology
Function and homology information


negative regulation of bile acid biosynthetic process / betaKlotho-mediated ligand binding / fibroblast growth factor receptor binding / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / neural crest cell migration / PI-3K cascade:FGFR4 / PI3K Cascade / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR4 ...negative regulation of bile acid biosynthetic process / betaKlotho-mediated ligand binding / fibroblast growth factor receptor binding / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / neural crest cell migration / PI-3K cascade:FGFR4 / PI3K Cascade / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR4 / FRS-mediated FGFR4 signaling / neurogenesis / regulation of cell migration / positive regulation of D-glucose import across plasma membrane / growth factor activity / response to bacterium / Negative regulation of FGFR4 signaling / positive regulation of JNK cascade / positive regulation of protein phosphorylation / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / nervous system development / heart development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / response to ethanol / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / negative regulation of gene expression / positive regulation of cell population proliferation / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Fibroblast growth factor 15/19/21 / 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 / Immunoglobulins ...Fibroblast growth factor 15/19/21 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor 19
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59775753879 Å
AuthorsLiu, H. / Zheng, S. / Hou, X. / Liu, X. / Lv, X. / Li, Y. / Li, W. / Sui, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China) China
CitationJournal: Cancer Sci. / Year: 2020
Title: Novel Abs targeting the N-terminus of fibroblast growth factor 19 inhibit hepatocellular carcinoma growth without bile-acid-related side-effects.
Authors: Liu, H. / Zheng, S. / Hou, X. / Liu, X. / Du, K. / Lv, X. / Li, Y. / Yang, F. / Li, W. / Sui, J.
History
DepositionAug 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.2Oct 23, 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: G1A8-Fab-HC
B: G1A8-Fab-LC
C: Fibroblast growth factor 19
D: Fibroblast growth factor 19
F: G1A8-Fab-HC
G: G1A8-Fab-LC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,32819
Polymers144,2996
Non-polymers1,03013
Water4,774265
1
A: G1A8-Fab-HC
B: G1A8-Fab-LC
C: Fibroblast growth factor 19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6308
Polymers72,1493
Non-polymers4805
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-93 kcal/mol
Surface area24980 Å2
MethodPISA
2
D: Fibroblast growth factor 19
F: G1A8-Fab-HC
G: G1A8-Fab-LC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,69911
Polymers72,1493
Non-polymers5498
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-128 kcal/mol
Surface area25090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.968, 104.125, 165.365
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules CD

#3: Protein Fibroblast growth factor 19 / FGF-19


Mass: 24556.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF19, UNQ334/PRO533 / Production host: Homo sapiens (human) / References: UniProt: O95750

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Antibody , 2 types, 4 molecules AFBG

#1: Antibody G1A8-Fab-HC


Mass: 24876.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-F / Production host: Homo sapiens (human)
#2: Antibody G1A8-Fab-LC


Mass: 22715.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-F / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 278 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 0.2M Lithium Sulfate monohydrate, 0.1M Bis-Tris pH6.9, 26% w/v Polyethylene Glycol 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.59→48.73 Å / Num. obs: 45911 / % possible obs: 99.7 % / Redundancy: 2 % / Biso Wilson estimate: 57.8977970902 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.017 / Rpim(I) all: 0.017 / Rsym value: 0.024 / Net I/σ(I): 3.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4486 / CC1/2: 0.952 / Rpim(I) all: 0.145 / Rrim(I) all: 0.205 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P23

2p23


Resolution: 2.59775753879→48.7165078095 Å / SU ML: 0.415182139297 / Cross valid method: FREE R-VALUE / σ(F): 1.37685714956 / Phase error: 27.0492811013
RfactorNum. reflection% reflection
Rfree0.253189839371 2000 4.36357289349 %
Rwork0.202012085943 --
obs0.204167575911 45834 99.6607958252 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 64.8763097796 Å2
Refinement stepCycle: LAST / Resolution: 2.59775753879→48.7165078095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8422 0 53 265 8740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002576323609648674
X-RAY DIFFRACTIONf_angle_d0.58653627154911809
X-RAY DIFFRACTIONf_chiral_restr0.04423438881031307
X-RAY DIFFRACTIONf_plane_restr0.004595290288361504
X-RAY DIFFRACTIONf_dihedral_angle_d6.296606668855105
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5978-2.66270.4097222238291390.3518931735933068X-RAY DIFFRACTION98.8289676425
2.6627-2.73470.3696232560551420.2937508511853084X-RAY DIFFRACTION99.5371798828
2.7347-2.81520.3344059842271400.268246149143083X-RAY DIFFRACTION99.3832870799
2.8152-2.9060.3157512594931400.2495173276373065X-RAY DIFFRACTION99.6269816599
2.906-3.00990.3150518007021410.2491253601323093X-RAY DIFFRACTION99.6610169492
3.0099-3.13040.3270493967521430.2589280195573108X-RAY DIFFRACTION99.6627835684
3.1304-3.27280.2782680533121410.2548714092323116X-RAY DIFFRACTION99.7549770291
3.2728-3.44530.3132318307921430.2328335148263124X-RAY DIFFRACTION99.9388192108
3.4453-3.66110.3071879174531420.2154790369153096X-RAY DIFFRACTION99.84582177
3.6611-3.94370.2628299200841420.1959731755083137X-RAY DIFFRACTION99.8477466504
3.9437-4.34030.2187462114951450.1651369364333173X-RAY DIFFRACTION100
4.3403-4.96780.1639225622191440.1452618498393159X-RAY DIFFRACTION99.9697336562
4.9678-6.25690.2117987938271450.1696131460043188X-RAY DIFFRACTION99.7307001795
6.2569-48.710.2195965742921530.1853753741133340X-RAY DIFFRACTION99.5156695157

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