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- PDB-6jfv: The crystal structure of 2B-2B complex from keratins 5 and 14 (C3... -

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Basic information

Entry
Database: PDB / ID: 6jfv
TitleThe crystal structure of 2B-2B complex from keratins 5 and 14 (C367A mutant of K14)
Components
  • Keratin, type I cytoskeletal 14
  • Keratin, type II cytoskeletal 5
KeywordsCYTOSOLIC PROTEIN / Intermediate filaments / Keratinocytes / Skin / Epithelium / Protein Self-assembly
Function / homology
Function and homology information


intermediate filament polymerization / intermediate filament bundle assembly / structural constituent of skin epidermis / Type I hemidesmosome assembly / keratin filament / Keratinization / keratin filament binding / hair cycle / intermediate filament organization / Formation of the cornified envelope ...intermediate filament polymerization / intermediate filament bundle assembly / structural constituent of skin epidermis / Type I hemidesmosome assembly / keratin filament / Keratinization / keratin filament binding / hair cycle / intermediate filament organization / Formation of the cornified envelope / basal part of cell / cornified envelope / intermediate filament / keratinization / epidermis development / response to mechanical stimulus / keratinocyte differentiation / regulation of cell migration / epithelial cell differentiation / stem cell differentiation / structural constituent of cytoskeleton / regulation of protein localization / scaffold protein binding / cytoskeleton / extracellular exosome / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Keratin, type I / Keratin, type II / Keratin type II head / Keratin type II head / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein
Similarity search - Domain/homology
Keratin, type I cytoskeletal 14 / Keratin, type II cytoskeletal 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsKim, M.S. / Lee, C.H. / Coulombe, P.A. / Leahy, D.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: Structure / Year: 2020
Title: Structure-Function Analyses of a Keratin Heterotypic Complex Identify Specific Keratin Regions Involved in Intermediate Filament Assembly.
Authors: Lee, C.H. / Kim, M.S. / Li, S. / Leahy, D.J. / Coulombe, P.A.
History
DepositionFeb 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Structure summary / Category: citation / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Keratin, type I cytoskeletal 14
B: Keratin, type II cytoskeletal 5
C: Keratin, type I cytoskeletal 14
D: Keratin, type II cytoskeletal 5


Theoretical massNumber of molelcules
Total (without water)45,0624
Polymers45,0624
Non-polymers00
Water1448
1
A: Keratin, type I cytoskeletal 14
B: Keratin, type II cytoskeletal 5


Theoretical massNumber of molelcules
Total (without water)22,5312
Polymers22,5312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-58 kcal/mol
Surface area14090 Å2
MethodPISA
2
C: Keratin, type I cytoskeletal 14
D: Keratin, type II cytoskeletal 5


Theoretical massNumber of molelcules
Total (without water)22,5312
Polymers22,5312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-58 kcal/mol
Surface area14290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.149, 56.149, 222.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Keratin, type I cytoskeletal 14 / ketatin(KRT14) / type II cytoskeletal 14 / Cytokeratin-14 / CK-14 / Keratin-14 / K14


Mass: 11132.647 Da / Num. of mol.: 2 / Mutation: C367A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRT14 / Production host: Escherichia coli (E. coli) / References: UniProt: P02533
#2: Protein Keratin, type II cytoskeletal 5 / 58 kDa cytokeratin / Cytokeratin-5 / CK-5 / Keratin-5 / K5 / Type-II keratin Kb5


Mass: 11398.142 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRT5 / Production host: Escherichia coli (E. coli) / References: UniProt: P13647
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.95 Å3/Da / Density % sol: 68.86 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 12%(w/v) PEG-8000, 0.1M sodium cacodylate pH 6.5, and 0.2 M calcium acetate hydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97838 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97838 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.496
ReflectionResolution: 2.6→37.38 Å / Num. obs: 20216 / % possible obs: 96.08 % / Redundancy: 4.6 % / Net I/σ(I): 8.91
Reflection shellResolution: 2.6→2.69 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementResolution: 2.6→37.38 Å / Cross valid method: FREE R-VALUE / σ(F): 0.14 / Phase error: 29.32
RfactorNum. reflection% reflection
Rfree0.2458 1040 5.14 %
Rwork0.2007 --
obs0.203 20216 95.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 98.433 Å2 / ksol: 0.295 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--13.8117 Å2-0 Å2-0 Å2
2---13.8117 Å2-0 Å2
3----2.4734 Å2
Refinement stepCycle: LAST / Resolution: 2.6→37.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3079 0 0 8 3087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063087
X-RAY DIFFRACTIONf_angle_d0.7594117
X-RAY DIFFRACTIONf_dihedral_angle_d18.5091257
X-RAY DIFFRACTIONf_chiral_restr0.046470
X-RAY DIFFRACTIONf_plane_restr0.002542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5984-2.69120.4405930.39461769X-RAY DIFFRACTION98
2.6912-2.79890.3562960.36111852X-RAY DIFFRACTION98
2.7989-2.92630.3386980.32371848X-RAY DIFFRACTION98
2.9263-3.08050.28041000.27871890X-RAY DIFFRACTION98
3.0805-3.27340.311020.27181946X-RAY DIFFRACTION98
3.2734-3.52590.331030.26081949X-RAY DIFFRACTION98
3.5259-3.88040.25691010.20051936X-RAY DIFFRACTION98
3.8804-4.44120.18861070.1622003X-RAY DIFFRACTION98
4.4412-5.59240.19161040.15592014X-RAY DIFFRACTION98
5.5924-37.38870.21311060.1411999X-RAY DIFFRACTION98
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)
15.5911-2.2053-2.41855.4522-3.5836-3.2553-0.1496-0.2057-0.0186-1.0601-0.8506-0.40380.1248-0.64030.08931.1862-0.0085-0.17761.3573-0.02720.272621.7828-10.961554.3581
23.9325-1.9074-0.28637.66112.4545-3.48920.6997-0.6732-0.044-0.3284-0.63610.08280.36640.33450.05731.11170.0945-0.07291.414-0.00710.496420.5081.430732.1759
30.5563-2.2995-0.51497.19984.62860.0944-0.19021.1028-0.78210.0038-0.2256-0.43490.2322-1.33420.16081.3701-0.06320.03491.4602-0.10630.302817.601313.720513.0655
41.29090.9926-2.7272-0.5223-0.80215.5633-0.0592-0.0317-0.0972-0.25250.3791-0.18470.77780.1707-0.12360.7113-0.0299-0.01651.28540.11260.120518.277741.6724-21.9613
50.0807-0.33890.17970.3174-1.81741.1608-2.0441-1.17950.7694-0.7961.41760.28640.2052-0.1671-0.02441.82630.09850.01382.1099-0.14470.714833.1071-14.610157.1266
60.22390.00882.13613.01622.98837.09270.03060.33040.512-0.01220.4787-1.89090.39590.8159-0.53631.17720.1081-0.09341.297-0.15540.592328.49180.146743.7922
70.05252.3903-1.0193-0.5999-0.34176.7303-0.3596-0.58870.40420.1450.0545-0.78350.0961-2.5671-0.08481.39290.030.02231.140.02190.378817.926524.130213.7133
84.02560.2952-0.67893.668-1.57280.23640.4150.13490.44530.10990.61270.67220.5860.14890.14851.00410.13980.02521.30860.14470.521310.030546.0644-27.604
96.3742-0.827-2.12952.298-1.40362.3185-0.36991.0221-0.7066-0.02650.780.05990.0710.6221-0.29761.4069-0.0679-0.10261.27650.07620.5152-36.06349.4231-47.3376
105.9-2.1751-0.3751.3522-0.51520.25730.3420.0540.1039-0.4727-0.3143-0.2451.3696-0.07350.04911.3128-0.0633-0.06491.130.04970.3244-13.675746.2699-9.9202
11-0.1932.6566-0.84892.22391.83196.4802-0.04130.8144-0.6647-0.26880.678-0.36161.18510.5422-0.22341.5201-0.1042-0.11651.0573-0.07250.26267.414347.356117.15
123.4507-0.89630.97333.58161.9546-1.31490.4322-0.29960.6829-0.7080.1847-0.06480.48280.2385-0.06961.47760.0119-0.17261.2995-0.19160.642725.436545.335835.6457
13-1.0384-0.6041.36390.9473-1.79290.0370.7293-0.3264-0.568-0.53620.04830.2353-0.91820.66070.04762.0658-1.5081-1.31395.93512.32452.1246-47.972862.5445-60.5032
141.51841.6542-3.37890.9905-3.59124.76870.75161.66270.79880.01950.0191-0.42560.6405-0.8327-0.56171.31770.0992-0.07451.74690.13230.4965-28.508356.6391-42.3712
155.35460.9018-3.05622.28691.36922.57480.10430.11350.2423-0.0359-0.3065-0.2140.3401-0.5135-0.30551.1693-0.10080.01261.2453-0.07350.2758-4.291646.342-13.1741
163.75570.31022.90212.86731.08630.92470.2805-0.18090.54410.1456-0.3087-0.3241.9839-0.8006-0.09831.33190.1401-0.23741.0767-0.10530.513716.327538.31826.3165
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 327:347)
2X-RAY DIFFRACTION2(chain A and resid 348:360)
3X-RAY DIFFRACTION3(chain A and resid 361:378)
4X-RAY DIFFRACTION4(chain A and resid 379:419)
5X-RAY DIFFRACTION5(chain B and resid 384:391)
6X-RAY DIFFRACTION6(chain B and resid 392:411)
7X-RAY DIFFRACTION7(chain B and resid 412:443)
8X-RAY DIFFRACTION8(chain B and resid 444:476)
9X-RAY DIFFRACTION9(chain C and resid 329:354)
10X-RAY DIFFRACTION10(chain C and resid 355:386)
11X-RAY DIFFRACTION11(chain C and resid 387:399)
12X-RAY DIFFRACTION12(chain C and resid 400:421)
13X-RAY DIFFRACTION13(chain D and resid 379:387)
14X-RAY DIFFRACTION14(chain D and resid 388:415)
15X-RAY DIFFRACTION15(chain D and resid 416:438)
16X-RAY DIFFRACTION16(chain D and resid 439:476)

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