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- PDB-6e2j: Crystal structure of the heterocomplex between human keratin 1 co... -

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Basic information

Entry
Database: PDB / ID: 6e2j
TitleCrystal structure of the heterocomplex between human keratin 1 coil 1B containing S233L mutation and wild-type human keratin 10 coil 1B
Components
  • Keratin, type I cytoskeletal 10
  • Keratin, type II cytoskeletal 1
KeywordsPROTEIN FIBRIL / intermediate filament / keratin / coiled-coil / skin
Function / homology
Function and homology information


positive regulation of epidermis development / structural constituent of skin epidermis / keratin filament / Keratinization / complement activation, lectin pathway / intermediate filament organization / Formation of the cornified envelope / peptide cross-linking / cornified envelope / protein heterotetramerization ...positive regulation of epidermis development / structural constituent of skin epidermis / keratin filament / Keratinization / complement activation, lectin pathway / intermediate filament organization / Formation of the cornified envelope / peptide cross-linking / cornified envelope / protein heterotetramerization / intermediate filament / keratinization / epidermis development / establishment of skin barrier / regulation of angiogenesis / keratinocyte differentiation / epithelial cell differentiation / fibrinolysis / negative regulation of inflammatory response / signaling receptor activity / carbohydrate binding / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / response to oxidative stress / blood microparticle / cytoskeleton / protein heterodimerization activity / Neutrophil degranulation / cell surface / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Keratin type II cytoskeletal 1, tail / Keratin type II cytoskeletal 1 tail / 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 ...Keratin type II cytoskeletal 1, tail / Keratin type II cytoskeletal 1 tail / 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 II cytoskeletal 1 / Keratin, type I cytoskeletal 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.386 Å
AuthorsEldirany, S.A. / Lomakin, I.B. / Bunick, C.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)K08-AR070290 United States
Other privateFoundation for Ichthyosis & Related Skin Types United States
CitationJournal: Embo J. / Year: 2019
Title: Human keratin 1/10-1B tetramer structures reveal a knob-pocket mechanism in intermediate filament assembly.
Authors: Eldirany, S.A. / Ho, M. / Hinbest, A.J. / Lomakin, I.B. / Bunick, C.G.
History
DepositionJul 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Keratin, type II cytoskeletal 1
B: Keratin, type I cytoskeletal 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2966
Polymers24,9122
Non-polymers3844
Water1,08160
1
A: Keratin, type II cytoskeletal 1
B: Keratin, type I cytoskeletal 10
hetero molecules

A: Keratin, type II cytoskeletal 1
B: Keratin, type I cytoskeletal 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,59212
Polymers49,8244
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area17070 Å2
ΔGint-238 kcal/mol
Surface area26420 Å2
MethodPISA
2
A: Keratin, type II cytoskeletal 1
B: Keratin, type I cytoskeletal 10
hetero molecules

A: Keratin, type II cytoskeletal 1
B: Keratin, type I cytoskeletal 10
hetero molecules

A: Keratin, type II cytoskeletal 1
B: Keratin, type I cytoskeletal 10
hetero molecules

A: Keratin, type II cytoskeletal 1
B: Keratin, type I cytoskeletal 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,18424
Polymers99,6478
Non-polymers1,53716
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area39160 Å2
ΔGint-506 kcal/mol
Surface area47830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.296, 93.296, 124.742
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11B-416-

HOH

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Components

#1: Protein Keratin, type II cytoskeletal 1 / / 67 kDa cytokeratin / Cytokeratin-1 / CK-1 / Hair alpha protein / Keratin-1 / K1 / Type-II keratin Kb1


Mass: 12790.273 Da / Num. of mol.: 1 / Mutation: S233L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRT1, KRTA / Production host: Escherichia coli (E. coli) / References: UniProt: P04264
#2: Protein Keratin, type I cytoskeletal 10 / / Cytokeratin-10 / CK-10 / Keratin-10 / K10


Mass: 12121.534 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRT10, KPP / Production host: Escherichia coli (E. coli) / References: UniProt: P13645
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.15 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, 1.5 M ammonium sulfate, 12% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.386→50 Å / Num. obs: 13342 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 67.3 Å2 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.04 / Rrim(I) all: 0.145 / Χ2: 1.061 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.39-2.43100.9696340.7870.3091.0190.72799.5
2.43-2.4810.90.9046610.7930.2790.9480.747100
2.48-2.5211.70.896470.8350.2690.9310.766100
2.52-2.5711.30.726260.9090.2220.7540.806100
2.57-2.6313.60.7116560.8880.20.740.793100
2.63-2.6914.40.556560.9360.150.570.859100
2.69-2.7614.10.5046550.9470.140.5240.92100
2.76-2.8314.30.4176660.9640.1160.4330.97100
2.83-2.9214.20.3346480.980.0920.3461.11100
2.92-3.0113.90.3086520.970.0870.3211.15799.8
3.01-3.1212.80.276630.9750.0790.2811.131100
3.12-3.2413.60.2366550.9770.0670.2461.229100
3.24-3.3914.70.2026550.9880.0550.211.247100
3.39-3.5714.50.1776660.9890.0480.1841.264100
3.57-3.7914.20.1586690.9910.0440.1641.314100
3.79-4.0913.30.1366790.9920.0390.1421.21199.9
4.09-4.513.90.136790.9920.0370.1351.21299.9
4.5-5.1514.30.1216840.9960.0350.1261.199100
5.15-6.4813.10.1297080.9940.0370.1341.1399.9
6.48-5012.20.0977830.9980.0290.1021.09699.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.386→46.648 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.49
RfactorNum. reflection% reflection
Rfree0.2943 699 5.26 %
Rwork0.2711 --
obs0.2723 13278 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 345.49 Å2 / Biso mean: 106.3133 Å2 / Biso min: 51.09 Å2
Refinement stepCycle: final / Resolution: 2.386→46.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 20 60 1823
Biso mean--164.14 91.8 -
Num. residues----211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041783
X-RAY DIFFRACTIONf_angle_d0.5872400
X-RAY DIFFRACTIONf_chiral_restr0.029268
X-RAY DIFFRACTIONf_plane_restr0.005315
X-RAY DIFFRACTIONf_dihedral_angle_d17.4081117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3856-2.56970.37181330.34912403253698
2.5697-2.82830.40681310.360324912622100
2.8283-3.23750.39021370.351124872624100
3.2375-4.07850.30551410.270225302671100
4.0785-46.65690.24721570.23372668282599
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)
18.04971.23410.80610.46050.61780.9058-0.10580.94510.44651.0281-0.02941.7106-0.2921-0.80780.46430.59830.22660.23051.06660.37431.216-33.344667.251917.5596
25.0631-1.1122-3.73816.22475.64087.0924-0.1261-2.0028-0.48120.71011.30160.3452-0.22540.1723-1.90340.6899-0.04240.1961.13130.1751.141-20.717760.113713.7148
37.2277-5.5095-2.543410.031-0.55394.7470.76950.80590.1817-1.0362-0.5725-0.7361-0.2907-0.0205-0.60850.52410.1314-0.00860.8095-0.00060.6599-5.369347.047510.2216
42.42431.6850.01657.9828-4.42833.17240.96180.89041.1836-1.8491-1.1728-1.16580.8764-0.3279-0.15970.95210.34060.31511.0322-0.08661.1569.634735.38269.7723
53.4011-4.9182-1.25437.41561.53152.0251.46311.10221.0783-1.6646-0.7186-0.5238-0.0413-0.2998-0.39050.56770.15950.06631.0208-0.10190.619218.93927.21619.9316
64.4527-3.4740.76563.9633-0.41611.1469-0.2851-0.8129-1.09990.41440.56210.10080.35390.1182-0.09090.4940.17220.01610.8216-0.22620.480145.842314.891512.1332
78.71112.37232.14948.822-0.12014.39040.3978-0.8443-1.59691.2712-0.2424-0.03260.6491-0.43660.07760.60160.4625-0.1780.8866-0.47350.788572.42685.965313.7382
83.6706-3.41983.52461.9946-6.20444.77620.71290.01330.6978-0.4124-1.4959-2.57180.48462.19020.95980.8770.3216-0.34931.2047-0.24361.26183.46971.409513.7448
90.9859-0.44630.42230.2042-0.00625.44080.234-0.2706-1.1394-0.35970.15130.93540.54630.699-0.64111.03721.1515-1.04352.5682-0.66471.975990.576-3.990813.9034
109.51342.2411.99448.818-3.97892.99420.2816-2.862-1.2693-1.48940.41061.23830.5438-3.02220.57230.7595-0.05030.08671.91550.45331.475-41.228761.012417.0706
111.0473-0.47660.81780.83770.62813.4837-0.2083-1.07460.6870.71730.12641.14660.6658-0.7377-0.14660.77740.11230.32351.10230.44791.592-30.069454.843319.1092
127.9895-3.00270.23755.64771.91772.7260.5787-0.61290.3778-0.24290.2482-0.17280.0927-0.0145-0.89380.63960.07760.11450.87440.09020.5289-8.198945.893218.9405
134.7397-0.44850.9261.90661.29231.0950.19590.04162.3503-2.13670.5733-2.0521-1.0020.2773-0.71560.62830.10120.3350.8851-0.37711.622518.361436.024314.7386
145.19320.666-4.39182.5020.74686.2155-0.19180.60254.27260.30380.9637-0.5440.5253-1.2465-0.44890.60720.06960.0271.0084-0.11870.984934.533427.91678.5687
152.2626-2.418-1.29643.54050.43069.22530.6546-1.4061.1095-0.39830.06340.1418-0.20510.3013-0.36390.43070.02510.01570.8859-0.14220.712746.167320.85755.308
167.6005-3.0929-0.96766.8953-0.4771.3050.75010.7469-0.0023-1.3648-0.0776-0.2999-0.0495-0.1795-0.57320.43310.03780.00020.9947-0.31880.630261.98118.51313.4525
170.5815-1.26660.35973.1163-1.30482.88890.76481.0352-0.56820.36940.252-2.58011.88562.0711-0.34630.31110.8464-0.37490.8558-0.83861.793376.136-2.88836.1846
184.48463.5516-0.69158.4447-6.65456.7269-1.96520.2366-1.5493-0.6939-2.5380.38720.5756-2.76963.23981.54570.09580.42721.4519-0.15431.568984.3432-9.70946.1697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 225:238)A225 - 238
2X-RAY DIFFRACTION2(chain A and resid 239:244)A239 - 244
3X-RAY DIFFRACTION3(chain A and resid 245:264)A245 - 264
4X-RAY DIFFRACTION4(chain A and resid 265:270)A265 - 270
5X-RAY DIFFRACTION5(chain A and resid 271:281)A271 - 281
6X-RAY DIFFRACTION6(chain A and resid 282:309)A282 - 309
7X-RAY DIFFRACTION7(chain A and resid 310:319)A310 - 319
8X-RAY DIFFRACTION8(chain A and resid 320:325)A320 - 325
9X-RAY DIFFRACTION9(chain A and resid 326:331)A326 - 331
10X-RAY DIFFRACTION10(chain B and resid 193:199)B193 - 199
11X-RAY DIFFRACTION11(chain B and resid 200:210)B200 - 210
12X-RAY DIFFRACTION12(chain B and resid 211:230)B211 - 230
13X-RAY DIFFRACTION13(chain B and resid 231:248)B231 - 248
14X-RAY DIFFRACTION14(chain B and resid 249:256)B249 - 256
15X-RAY DIFFRACTION15(chain B and resid 257:267)B257 - 267
16X-RAY DIFFRACTION16(chain B and resid 268:282)B268 - 282
17X-RAY DIFFRACTION17(chain B and resid 283:291)B283 - 291
18X-RAY DIFFRACTION18(chain B and resid 292:296)B292 - 296

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