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- PDB-6nfj: Structure of Beta-Klotho in Complex with FGF19 C-terminal peptide -

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Open data


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Basic information

Entry
Database: PDB / ID: 6nfj
TitleStructure of Beta-Klotho in Complex with FGF19 C-terminal peptide
Components
  • Beta-klotho
  • Fibroblast growth factor 19
  • Nanobody 30
KeywordsSIGNALING PROTEIN / Klotho / FGF19 / Nanobody / receptor tyrosine kinase / signaling
Function / homology
Function and homology information


negative regulation of bile acid biosynthetic process / betaKlotho-mediated ligand binding / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / fibroblast growth factor receptor binding / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / fibroblast growth factor binding / PI-3K cascade:FGFR4 / PI3K Cascade / fibroblast growth factor receptor signaling pathway ...negative regulation of bile acid biosynthetic process / betaKlotho-mediated ligand binding / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / fibroblast growth factor receptor binding / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / fibroblast growth factor binding / PI-3K cascade:FGFR4 / PI3K Cascade / fibroblast growth factor receptor signaling pathway / hydrolase activity, hydrolyzing O-glycosyl compounds / SHC-mediated cascade:FGFR4 / FRS-mediated FGFR4 signaling / regulation of cell migration / positive regulation of glucose import / Negative regulation of FGFR4 signaling / animal organ morphogenesis / positive regulation of JNK cascade / growth factor activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / nervous system development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / carbohydrate metabolic process / cell differentiation / positive regulation of ERK1 and ERK2 cascade / positive regulation of protein phosphorylation / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / plasma membrane / 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 / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Fibroblast growth factor 19 / Beta-klotho
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsKuzina, E. / Schlessinger, J. / Lee, S.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Structures of ligand-occupied beta-Klotho complexes reveal a molecular mechanism underlying endocrine FGF specificity and activity.
Authors: Kuzina, E.S. / Ung, P.M. / Mohanty, J. / Tome, F. / Choi, J. / Pardon, E. / Steyaert, J. / Lax, I. / Schlessinger, A. / Schlessinger, J. / Lee, S.
History
DepositionDec 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-klotho
B: Nanobody 30
C: Fibroblast growth factor 19
D: Beta-klotho
E: Nanobody 30
F: Fibroblast growth factor 19


Theoretical massNumber of molelcules
Total (without water)261,2856
Polymers261,2856
Non-polymers00
Water00
1
A: Beta-klotho
B: Nanobody 30
C: Fibroblast growth factor 19


Theoretical massNumber of molelcules
Total (without water)130,6433
Polymers130,6433
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Beta-klotho
E: Nanobody 30
F: Fibroblast growth factor 19


Theoretical massNumber of molelcules
Total (without water)130,6433
Polymers130,6433
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.090, 143.900, 141.050
Angle α, β, γ (deg.)90.00, 90.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-klotho / BetaKlotho / Klotho beta-like protein


Mass: 110389.242 Da / Num. of mol.: 2 / Mutation: N308Q, N611Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLB / Cell line (production host): 293-EBNA / Production host: Homo sapiens (human) / References: UniProt: Q86Z14
#2: Antibody Nanobody 30


Mass: 14700.269 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Strain (production host): WK6
#3: Protein/peptide Fibroblast growth factor 19 / FGF-19


Mass: 5553.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O95750

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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: 51.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 21% PEG1500, 0.1M Ammonium sulphate, 0.2M NDSB-201, 0.1M Tris-HCl pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.19→59.42 Å / Num. obs: 42869 / % possible obs: 99.23 % / Redundancy: 3.8 % / Net I/σ(I): 3.4
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 0.81 / CC1/2: 0.519 / % possible all: 95.87

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
PHASERphasing
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VAQ
Resolution: 3.19→59.42 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.64
RfactorNum. reflection% reflection
Rfree0.3196 3849 4.64 %
Rwork0.2796 --
obs0.2815 42869 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.19→59.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14271 0 0 0 14271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214697
X-RAY DIFFRACTIONf_angle_d0.44620110
X-RAY DIFFRACTIONf_dihedral_angle_d10.5398294
X-RAY DIFFRACTIONf_chiral_restr0.042187
X-RAY DIFFRACTIONf_plane_restr0.0032586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1935-3.23390.43631240.39282456X-RAY DIFFRACTION81
3.2339-3.27640.38431260.39172889X-RAY DIFFRACTION97
3.2764-3.32130.38971430.37112912X-RAY DIFFRACTION98
3.3213-3.36870.44441460.37573013X-RAY DIFFRACTION99
3.3687-3.4190.41011520.36442958X-RAY DIFFRACTION99
3.419-3.47240.36321480.35292975X-RAY DIFFRACTION99
3.4724-3.52940.36691450.35072963X-RAY DIFFRACTION99
3.5294-3.59020.38541490.34313032X-RAY DIFFRACTION99
3.5902-3.65550.36671440.33822854X-RAY DIFFRACTION99
3.6555-3.72580.34551410.31173104X-RAY DIFFRACTION99
3.7258-3.80180.32071400.30562894X-RAY DIFFRACTION99
3.8018-3.88450.36171470.28522975X-RAY DIFFRACTION98
3.8845-3.97480.3671350.27912919X-RAY DIFFRACTION98
3.9748-4.07420.32321480.26792958X-RAY DIFFRACTION99
4.0742-4.18430.32091350.2572953X-RAY DIFFRACTION99
4.1843-4.30740.27161440.25442938X-RAY DIFFRACTION98
4.3074-4.44640.31321450.2422925X-RAY DIFFRACTION98
4.4464-4.60530.2891460.23112959X-RAY DIFFRACTION98
4.6053-4.78960.27931440.23492860X-RAY DIFFRACTION96
4.7896-5.00750.26741440.23772932X-RAY DIFFRACTION98
5.0075-5.27130.251400.24462957X-RAY DIFFRACTION99
5.2713-5.60140.34451420.25622997X-RAY DIFFRACTION99
5.6014-6.03350.31351410.26052981X-RAY DIFFRACTION99
6.0335-6.63990.30231470.27272970X-RAY DIFFRACTION99
6.6399-7.5990.26591470.26652964X-RAY DIFFRACTION99
7.599-9.56750.26851380.23832945X-RAY DIFFRACTION97
9.5675-59.42440.32021480.27072907X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.04470.4454-0.16642.4228-0.21641.3102-0.0432-0.0294-0.0668-0.4894-0.0951-0.00250.2455-0.01010.11830.46030.07680.06590.34040.03521.4786-37.54160.80724.0188
21.2181-0.53530.32650.8008-0.25810.33530.0886-0.0420.2612-0.55320.0403-0.0577-0.1779-0.0583-0.08940.29390.06730.28960.3505-0.09991.1362-7.269337.266740.8877
32.5213-1.91950.47831.863-0.69260.4156-0.1364-0.0046-0.0810.0888-0.0553-0.4335-0.01050.16340.08190.45080.23450.12540.130.00750.69253.624220.029537.7959
40.9703-0.72980.27791.66930.16130.68910.19380.2980.0563-0.5887-0.2384-0.4625-0.09270.15750.00150.04970.2861-0.00030.10330.10940.7202-3.188225.681843.0687
53.96390.78114.67973.74690.45117.27830.73040.6097-0.3332-0.74380.4718-0.20250.3445-0.5667-1.04791.10010.186-0.14380.6515-0.0020.5949-24.50443.287417.8606
62.38651.49421.98851.31781.54294.784-0.2750.07250.131-0.5998-0.61830.739-0.1462-0.33650.49881.1251-0.23180.07150.5557-0.21740.6019-13.777.664427.4025
70.6856-0.3763-0.61751.3138-0.61813.8966-0.1608-0.0559-0.21660.1248-0.02410.25290.1086-0.3110.09590.39490.06520.25250.8573-0.21310.7351-12.157416.195625.0901
83.13980.97091.84658.04745.93535.4636-0.25610.03330.3904-1.4333-0.1429-0.0912-0.1220.27990.14871.25820.35410.0770.5065-0.04780.5087-17.194610.38711.0351
93.0201-4.0286-4.06347.06864.70396.0851-0.0460.3214-0.2669-0.512-0.61811.0018-0.5321-0.85660.4931.02350.3239-0.05080.64470.06971.7358-21.235420.069718.6857
103.88-2.0284-3.21044.68431.42012.67880.21450.37750.50140.0286-0.70480.91370.2210.16620.47321.24010.348-0.0741.2466-0.1370.9918-28.364215.064912.3786
112.5973-1.3109-2.74285.61242.87754.0411-0.4443-0.3661-0.59322.11750.27670.71820.6423-0.21690.45281.30340.42250.30740.7858-0.11870.8791-21.655714.207828.0289
129.6643-1.39893.42187.3067-3.23476.41490.25910.451-1.394-1.3248-0.29630.85421.18570.034-0.01221.55930.14140.07030.5152-0.0161.4365-24.89499.879921.0833
133.2566-2.5099-2.53242.33853.01534.76570.35892.0092-1.3024-1.3711-1.13550.71680.7876-1.4230.70791.05710.07780.0211.1176-0.49510.7121-30.56455.99276.3288
145.4923-2.64681.42023.2893-2.76752.5220.46740.4087-1.4587-1.1735-0.52891.15921.70130.67380.27241.2710.28790.24770.6333-0.07711.0931-18.91335.661712.9828
151.7354-0.05591.13724.1836-2.22941.8950.44360.8930.0125-0.9644-1.3655-1.15920.54451.23580.771.18610.34760.07390.78840.32580.5688-9.845917.978514.7164
164.26491.76724.24331.05572.02364.58950.43750.1357-1.60.26270.6137-0.36810.01870.5494-0.96550.77870.3777-0.03270.9052-0.05120.8181-13.90117.598414.5365
177.6395-2.81472.06266.14410.28644.3916-0.11980.48571.20460.25090.0404-0.94880.3821.51420.1430.46830.24610.09970.75270.08631.3679-12.687549.092529.3633
180.1966-0.27150.64042.7058-2.90323.8334-0.07841.57160.1414-0.6833-0.42191.09220.0263-0.05030.45010.64960.4194-0.15391.10370.10541.0028-0.07136.564138.3769
192.20620.2043-0.20612.3290.09191.1889-0.0567-0.07480.30230.51250.09610.21-0.1026-0.04630.02030.17130.0392-0.04420.3125-0.03210.0436-4.479296.483123.4382
202.0157-1.19070.10530.9825-0.00891.0889-0.2768-0.4752-0.41940.58190.4933-0.51970.05460.424-0.07290.57530.0547-0.2630.50620.04460.639112.835780.412636.9921
213.8462-0.82170.72342.5106-0.72472.5032-0.4901-0.89010.03880.39180.3049-0.3265-0.03590.31460.16120.97550.3025-0.06760.8802-0.08661.275135.335860.023343.3014
220.2076-0.82220.0434.4457-0.16221.1789-0.2452-0.0085-0.0242-0.14250.06960.09660.1195-0.02630.05661.22840.03220.18810.4690.04081.909320.059441.293623.9984
231.99350.2422-0.07931.0216-0.06331.22730.12890.3620.1731-0.29180.24440.139-0.035-0.7808-0.19811.0072-0.35220.29910.96840.1160.49140.805638.002714.1808
244.7731-0.70342.26432.3363-1.39324.0426-0.8612-0.55731.26770.95230.0663-0.30181.26620.02070.66291.24980.29550.22880.6674-0.08221.078619.725448.598226.1487
257.5123-1.22411.11672.2036-0.23250.1671-0.65260.64390.7457-1.0450.3836-0.49971.1112-0.40520.25371.3168-0.26970.19320.5309-0.24680.955814.901746.791511.3473
260.04840.107-0.00870.238-0.01930.0015-0.20790.20290.6944-0.1960.09770.3923-0.2014-0.04330.35070.6774-0.1516-0.4540.75250.48312.0811.247556.024818.9431
275.57920.4775-1.92983.84830.87850.9534-0.31661.23770.2866-0.0671-0.19441.18480.2281-0.72690.62610.8025-0.3133-0.31690.7318-0.15760.88434.342751.038811.9938
283.67981.55570.01540.89240.18930.143-0.1898-0.48170.23850.8316-0.0748-0.1467-0.9830.6150.12241.26940.1228-0.08510.63880.01010.324610.93148.631227.2501
296.3752.12544.77442.99630.78466.99350.13981.66530.2551-1.16730.09930.2556-0.11220.4189-0.28221.33720.027-0.03471.14690.38740.5031.868544.745113.0726
306.02091.4393-0.98526.74-1.70630.49940.60070.1286-0.1535-0.7042-0.25590.61490.6932-1.9334-0.38250.6293-0.2745-0.06141.468-0.31740.69259.650240.82339.2378
311.7152-0.4615-0.34230.4981-0.29240.4636-0.0615-0.26720.48350.19290.0431-0.0533-0.5878-0.3072-0.12811.08650.33520.24240.8595-0.37060.969421.812454.817317.4185
322.7737-0.758-1.52292.3028-2.01184.03590.02070.18690.25410.0301-0.4061-0.3215-0.07880.59490.27481.3176-0.38430.52181.08730.29621.235223.500352.117110.5237
335.9139-1.33427.36320.3076-1.68139.23370.9552-0.2058-0.4048-0.48860.1008-0.5041.437-0.4079-0.88490.8398-0.06340.06970.8324-0.37720.671417.451241.855414.9429
343.2643-0.63493.29274.24271.42737.663-0.6881-0.06732.6330.2727-0.0938-0.78150.08561.51060.92530.67030.14680.13380.9287-0.0281.62519.968985.048729.7196
350.11910.149-0.43561.2241-0.01521.86220.08850.1429-0.3576-0.0684-0.65690.13860.01950.77130.21021.5417-0.00150.56951.6654-0.15060.773332.486272.653538.4906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 53:371)
2X-RAY DIFFRACTION2(chain A and resid 372:691)
3X-RAY DIFFRACTION3(chain A and resid 692:767)
4X-RAY DIFFRACTION4(chain A and resid 768:968)
5X-RAY DIFFRACTION5(chain B and resid 1:20)
6X-RAY DIFFRACTION6(chain B and resid 21:27)
7X-RAY DIFFRACTION7(chain B and resid 28:34)
8X-RAY DIFFRACTION8(chain B and resid 35:47)
9X-RAY DIFFRACTION9(chain B and resid 48:59)
10X-RAY DIFFRACTION10(chain B and resid 60:69)
11X-RAY DIFFRACTION11(chain B and resid 70:75)
12X-RAY DIFFRACTION12(chain B and resid 76:82)
13X-RAY DIFFRACTION13(chain B and resid 83:90)
14X-RAY DIFFRACTION14(chain B and resid 91:96)
15X-RAY DIFFRACTION15(chain B and resid 97:108)
16X-RAY DIFFRACTION16(chain B and resid 109:121)
17X-RAY DIFFRACTION17(chain C and resid 191:202)
18X-RAY DIFFRACTION18(chain C and resid 203:213)
19X-RAY DIFFRACTION19(chain D and resid 53:360)
20X-RAY DIFFRACTION20(chain D and resid 361:608)
21X-RAY DIFFRACTION21(chain D and resid 609:968)
22X-RAY DIFFRACTION22(chain E and resid 1:7)
23X-RAY DIFFRACTION23(chain E and resid 8:20)
24X-RAY DIFFRACTION24(chain E and resid 21:34)
25X-RAY DIFFRACTION25(chain E and resid 35:47)
26X-RAY DIFFRACTION26(chain E and resid 48:59)
27X-RAY DIFFRACTION27(chain E and resid 60:69)
28X-RAY DIFFRACTION28(chain E and resid 70:79)
29X-RAY DIFFRACTION29(chain E and resid 80:86)
30X-RAY DIFFRACTION30(chain E and resid 87:95)
31X-RAY DIFFRACTION31(chain E and resid 96:104)
32X-RAY DIFFRACTION32(chain E and resid 105:109)
33X-RAY DIFFRACTION33(chain E and resid 110:121)
34X-RAY DIFFRACTION34(chain F and resid 191:202)
35X-RAY DIFFRACTION35(chain F and resid 203:213)

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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

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