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- PDB-6uui: Crystal structure of the heterocomplex between coil 2B domains of... -

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Basic information

Entry
Database: PDB / ID: 6uui
TitleCrystal structure of the heterocomplex between coil 2B domains of wild-type keratin 1 (KRT1) and keratin 10 (KRT10) containing mutation Cys401Ala
Components
  • Keratin, type I cytoskeletal 10
  • Keratin, type II cytoskeletal 1
KeywordsPROTEIN FIBRIL / intermediate filament / cytoskeleton / skin / coiled-coil
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 / response to oxidative stress / ficolin-1-rich granule lumen / cytoskeleton / blood microparticle / protein heterodimerization activity / Neutrophil degranulation / cell surface / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / cytoplasm / cytosol
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: 2.069 Å
AuthorsLomakin, 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)K08AR070290 United States
Other privateFoundation for Ichthyosis and Related Skin Types United States
CitationJournal: Yale J Biol Med / Year: 2020
Title: Crystal Structure of Keratin 1/10(C401A) 2B Heterodimer Demonstrates a Proclivity for the C-Terminus of Helix 2B to Form Higher Order Molecular Contacts.
Authors: Lomakin, I.B. / Hinbest, A.J. / Ho, M. / Eldirany, S.A. / Bunick, C.G.
History
DepositionOct 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.country / _pdbx_audit_support.funding_organization
Revision 1.2Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
C: Keratin, type II cytoskeletal 1
X: Keratin, type I cytoskeletal 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3374
Polymers27,9532
Non-polymers3842
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-54 kcal/mol
Surface area16400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.124, 100.124, 224.788
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Components on special symmetry positions
IDModelComponents
11C-656-

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: 13850.421 Da / Num. of mol.: 1 / Fragment: 2B domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRT1, KRTA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04264
#2: Protein Keratin, type I cytoskeletal 10 / Cytokeratin-10 / CK-10 / Keratin-10 / K10


Mass: 14102.493 Da / Num. of mol.: 1 / Fragment: 2B domain / Mutation: C401A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRT10, KPP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13645
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 5.85 Å3/Da / Density % sol: 78.97 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: Ammonium phosphate dibasic, Tris, N-octyl-B-D-glucoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 7, 2017
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.0689→100 Å / Num. obs: 41346 / % possible obs: 99.4 % / Redundancy: 10.5 % / Biso Wilson estimate: 58.7223753258 Å2 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.036 / Rrim(I) all: 0.116 / Χ2: 1.162 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.07-2.1110.76.29520040.1071.9786.6060.93798.6
2.11-2.1410.84.89420080.311.5365.1350.85598.9
2.14-2.1910.65.02920170.3211.5915.2810.86499
2.19-2.2310.53.93120160.4321.2524.1310.88199
2.23-2.2810.13.03720120.5790.9923.21.0798.7
2.28-2.339.62.24320190.6650.7482.3690.95199.1
2.33-2.39111.67220280.750.521.7530.8999.3
2.39-2.45111.22620190.7910.3781.2840.91699.4
2.45-2.5310.90.97120300.8680.3031.0180.96299.3
2.53-2.6110.80.66620430.9310.2090.6991.02399.6
2.61-2.710.60.53120590.9560.1690.5581.10899.5
2.7-2.819.80.42420470.9660.140.4471.14499.4
2.81-2.9410.60.29620630.9820.0950.3121.27999.6
2.94-3.0911.20.21120520.9880.0660.2211.3999.8
3.09-3.2910.90.16220770.9870.0510.171.54399.8
3.29-3.5410.60.12521090.9930.0410.1321.76299.8
3.54-3.910.10.10121080.9940.0330.1061.69599.7
3.9-4.4611.10.08321250.9950.0270.0881.64100
4.46-5.6210.10.0721700.9970.0230.0741.26199.6
5.62-10010.10.05723400.9980.020.0610.97799.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZRY

4zry


Resolution: 2.069→48.8648485788 Å / SU ML: 0.403595528138 / Cross valid method: THROUGHOUT / σ(F): 1.33335827305 / Phase error: 38.2322970729
RfactorNum. reflection% reflection
Rfree0.276910471286 2062 5.00315426797 %
Rwork0.250342981498 --
obs0.25174692579 41214 99.2653965654 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 123.819188818 Å2
Refinement stepCycle: LAST / Resolution: 2.069→48.8648485788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 26 107 1864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003858664976991785
X-RAY DIFFRACTIONf_angle_d0.6110128424972396
X-RAY DIFFRACTIONf_chiral_restr0.0293374473061280
X-RAY DIFFRACTIONf_plane_restr0.00241519526848318
X-RAY DIFFRACTIONf_dihedral_angle_d20.71106939921137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.069-2.1170.5001933762931330.4592496142372486X-RAY DIFFRACTION96.820702403
2.117-2.170.4703984543051260.4121699738252560X-RAY DIFFRACTION98.7137081955
2.17-2.22870.4642369100681310.4035945365072541X-RAY DIFFRACTION98.7800369686
2.2287-2.29420.423100081881080.3758898160142549X-RAY DIFFRACTION98.516870597
2.2942-2.36830.3545678149651490.3561764491132543X-RAY DIFFRACTION99.152854512
2.3683-2.45290.3588131561651210.3172119997712592X-RAY DIFFRACTION99.5596330275
2.4529-2.55110.3867214126091320.3315876544032583X-RAY DIFFRACTION99.4141340168
2.5511-2.66720.3008670926451420.3000053120442582X-RAY DIFFRACTION99.6706915477
2.6672-2.80790.2996436383651320.2893589431572603X-RAY DIFFRACTION99.4907238996
2.8079-2.98370.3200560398681270.2737950871622612X-RAY DIFFRACTION99.7450837582
2.9837-3.21410.3126547749591430.2941187564942637X-RAY DIFFRACTION99.9281092739
3.2141-3.53740.323497628011450.2604216480532636X-RAY DIFFRACTION99.964054637
3.5374-4.04910.2438326609291550.2154306833522647X-RAY DIFFRACTION99.8930481283
4.0491-5.10060.1973981494331570.1954984933952711X-RAY DIFFRACTION99.9303135889
5.1006-48.860.2758471279531610.2331989687312870X-RAY DIFFRACTION99.4422572178
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)
10.0197773633574-0.0132261200576-0.0224520702970.02002761846710.023484550640.02258790797760.2258452786170.296511870698-0.365792552575-0.1021162678880.0569738737085-0.2039869427260.3387893629530.0610632166168-0.001100693455062.06739863314-0.458626267333-0.581099125352.474046548510.4563703674583.05625172794-56.615842632972.8944651551310.302836835
20.0727509747970.0868930802482-0.1220341195070.118160039009-0.190750831860.26092892706-0.516333684374-0.8531039762690.4010377973581.6065181345-0.45655007751.50344011089-0.0713589172164-1.21295064239-0.01103385642540.971180870043-0.02037357630990.25799463331.32939496153-0.5640452102471.08000035032-51.320795371458.2194583144301.131315986
30.485054552726-0.656366940949-0.191975258042-0.1105951006641.09010432120.270411408234-0.146599522015-0.0243349078522-0.06700363251420.9976401350980.3288505890270.2076108661261.502436986350.912786118946-0.002982381876470.9105147594390.147675932645-0.08290647085380.858882057967-0.2561190891080.751890458743-39.421112584731.3890691745273.642843829
40.531675489365-0.256286164898-0.3883846816470.457561131946-0.04990141793870.473552140592-0.516641324584-0.504004269529-0.07144558240670.04024737973820.384735593037-0.1113023912620.2055340375620.675595299686-0.0002359691776690.7055511657660.12481635737-0.03084232956540.650987927823-0.0393589911030.573987744658-35.42268118680.95633718326236.288123374
51.82565156755-1.41645698791-0.8033523856271.893069195790.4276504848960.691510916579-0.8836339424151.43128090469-1.28271177937-1.09423463747-0.03663400903390.4309147684320.664515905186-0.930439223917-0.3768034316811.4536429045-0.4870598364990.3481405619031.05200291497-0.4398163610320.997707601647-45.4265093953-18.1071630647210.458786061
60.05633324865360.0511414094325-0.02462882572020.0449435149723-0.02341632820230.007318279265970.137029224384-0.106716801894-0.1022206989170.0356887187352-0.057669951263-0.0770067436602-0.09212349361060.325552087011-0.001367944588053.861110837971.28185868108-0.7058113905053.55521674525-0.1153836460821.90504977446-44.324818893375.1938858322314.753380178
70.607962270775-0.4142180810690.2893212337380.239363301507-0.1510496325280.151564979967-0.272272470617-0.2135386503440.8453092239220.196613179782-0.1793793490330.603683191449-1.148042657970.300056799607-0.005010125570330.945223136517-0.008055669597760.01286214863250.872540318055-0.4374620099751.11515118262-44.219761455164.5095285861297.889939647
8-0.4173083883180.01761740033230.1859277784150.0997261433388-0.2146772310790.6832487312540.2566198774710.2459548803970.0634094527581-1.12080180039-0.6823248510560.604348022489-0.568028326023-0.114291672334-0.001153197792160.6599660610450.290599214692-0.2435211287510.858632573311-0.3299980180940.812414877061-42.873098986536.9299474477267.387238576
91.172536450950.1418718947380.7245139484240.905543164831-0.4253213364051.13041588931-0.636138718785-0.5246446299740.0278481975660.502689094786-0.3664953034741.050616138340.401890235845-0.895632410055-0.007232636876030.7972731176360.1895777597510.04211897012820.701127948773-0.1167078837960.700837856177-44.9156849237-0.240470324592237.503416736
105.767395448091.432126550532.470259201911.45809848664-0.07487635523681.47301461439-0.1336270905791.07970564834-1.28115668528-0.8533130897190.509932194608-0.3467017938110.986282335913-0.2131552499110.3137059687021.98153153276-0.2172031259270.2140606851540.720801696204-0.1579267824771.02288589999-41.33913876-28.9864070443217.230058909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain C and resid 383:387)
2X-RAY DIFFRACTION2(chain C and resid 388:405)
3X-RAY DIFFRACTION3(chain C and resid 406:443)
4X-RAY DIFFRACTION4(chain C and resid 444:467)
5X-RAY DIFFRACTION5(chain C and resid 468:489)
6X-RAY DIFFRACTION6(chain X and resid 349:352)
7X-RAY DIFFRACTION7(chain X and resid 353:375)
8X-RAY DIFFRACTION8(chain X and resid 376:407)
9X-RAY DIFFRACTION9(chain X and resid 408:438)
10X-RAY DIFFRACTION10(chain X and resid 439:456)

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