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- PDB-4zry: Crystal structure of the heterocomplex between coil 2B domains of... -

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Basic information

Entry
Database: PDB / ID: 4zry
TitleCrystal structure of the heterocomplex between coil 2B domains of human intermediate filament proteins keratin 1 (KRT1) and keratin 10 (KRT10)
Components
  • Keratin, type I cytoskeletal 10
  • Keratin, type II cytoskeletal 1
KeywordsPROTEIN FIBRIL / keratin / intermediate filament / coiled-coil / skin / protein-protein complex / epidermis / helix
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: 3.30012502044 Å
AuthorsBunick, C.G. / Steitz, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Dermatology Foundation United States
CitationJournal: J. Invest. Dermatol. / Year: 2017
Title: The X-Ray Crystal Structure of the Keratin 1-Keratin 10 Helix 2B Heterodimer Reveals Molecular Surface Properties and Biochemical Insights into Human Skin Disease.
Authors: Bunick, C.G. / Milstone, L.M.
History
DepositionMay 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2017Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Keratin, type I cytoskeletal 10
B: Keratin, type II cytoskeletal 1


Theoretical massNumber of molelcules
Total (without water)28,2542
Polymers28,2542
Non-polymers00
Water0
1
A: Keratin, type I cytoskeletal 10
B: Keratin, type II cytoskeletal 1

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


Theoretical massNumber of molelcules
Total (without water)56,5094
Polymers56,5094
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-54 kcal/mol
Surface area15690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.190, 75.860, 209.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Keratin, type I cytoskeletal 10 / / Cytokeratin-10 / CK-10 / Keratin-10 / K10


Mass: 14403.900 Da / Num. of mol.: 1 / Fragment: coil 2B domain (UNP residues 337-456)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRT10, KPP / Plasmid: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) Codon + / References: UniProt: P13645
#2: 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: coil 2B domain (UNP residues 370-489)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRT1, KRTA / Plasmid: pGS21A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) Codon + / References: UniProt: P04264

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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: 5.28 Å3/Da / Density % sol: 79.7 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 2.0 M ammonium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.3→37.37 Å / Num. obs: 9336 / % possible obs: 99.6 % / Observed criterion σ(I): 0.5 / Redundancy: 6.4 % / Biso Wilson estimate: 156.426266325 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.76
Reflection shellResolution: 3.3→3.38 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 0.5 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
XDSdata reduction
XDSdata scaling
MOLREPphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3TNU

3tnu


Resolution: 3.30012502044→37.37 Å / Cross valid method: FREE R-VALUE / σ(F): 1.32610665852 / Phase error: 50.4833616336
RfactorNum. reflection% reflectionSelection details
Rfree0.276863469803 485 5.25119099177 %Random selection
Rwork0.272921078069 8751 --
obs0.273178625892 9236 98.5804248052 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 285.367408707 Å2
Refinement stepCycle: final / Resolution: 3.30012502044→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 0 0 1731
Num. residues----214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002990314686481737
X-RAY DIFFRACTIONf_angle_d0.6094220497532332
X-RAY DIFFRACTIONf_chiral_restr0.0254992360335274
X-RAY DIFFRACTIONf_plane_restr0.00125894508445311
X-RAY DIFFRACTIONf_dihedral_angle_d18.8091357396694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3001-3.77731532826X-RAY DIFFRACTION97.2893533638
3.7773-4.75740.3374404401561630.3326043394592877X-RAY DIFFRACTION98.7975300617
4.7574-37.370.2371992490431690.228534620343048X-RAY DIFFRACTION99.5975232198
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)
12.082645642920.5327240613540.1374382620382.388801773430.5724703385590.5970020131931.07770339915-0.394899664182-0.63331323380.922384931813-0.558236553807-0.1404963695932.47722672503-0.8659123414860.3251120483651.73051053672-0.0500675928541-0.05359274268751.2160718901-0.1938654160551.4618296914371.20821770185.8277909786445.5975306367
22.07901187302-0.452313464278-0.38651991280.371781179156-0.06992306926341.28480427836-0.339162413873-0.2849261184320.0819036711827-0.356002023765-0.687775415040.491468381035-0.732821714081-0.494839506529-0.1517563756550.812191908402-0.02244610067190.03867093328080.486705127856-0.2135187223380.85769905217371.29078794518.3551255803548.8477848934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 347 through 456 )
2X-RAY DIFFRACTION2chain 'B' and (resid 386 through 489 )

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