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- PDB-3tnu: Heterocomplex of coil 2B domains of human intermediate filament p... -

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Basic information

Entry
Database: PDB / ID: 3tnu
TitleHeterocomplex of coil 2B domains of human intermediate filament proteins, keratin 5 (KRT5) and keratin 14 (KRT14)
Components
  • Keratin, type I cytoskeletal 14
  • Keratin, type II cytoskeletal 5
KeywordsCYTOSOLIC PROTEIN / Coiled-coil / Structural Support
Function / homology
Function and homology information


intermediate filament polymerization / intermediate filament bundle assembly / structural constituent of skin epidermis / keratin filament / Type I hemidesmosome assembly / keratin filament binding / Keratinization / hair cycle / intermediate filament organization / Formation of the cornified envelope ...intermediate filament polymerization / intermediate filament bundle assembly / structural constituent of skin epidermis / keratin filament / Type I hemidesmosome assembly / keratin filament binding / Keratinization / hair cycle / intermediate filament organization / Formation of the cornified envelope / basal part of cell / cornified envelope / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / intermediate filament / keratinization / epidermis development / response to mechanical stimulus / keratinocyte differentiation / epithelial cell differentiation / regulation of cell migration / stem cell differentiation / structural constituent of cytoskeleton / regulation of protein localization / scaffold protein binding / cytoskeleton / extracellular exosome / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Keratin, type II / Keratin type II head / Keratin type II head / Keratin, type I / 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 ...Keratin, type II / Keratin type II head / Keratin type II head / Keratin, type I / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
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 / SAD / Resolution: 3.005 Å
AuthorsLee, C.H. / Kim, M.S. / Leahy, D.J. / Coulombe, P.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural basis for heteromeric assembly and perinuclear organization of keratin filaments.
Authors: Lee, C.H. / Kim, M.S. / Chung, B.M. / Leahy, D.J. / Coulombe, P.A.
History
DepositionSep 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)30,3992
Polymers30,3992
Non-polymers00
Water1086
1
A: Keratin, type I cytoskeletal 14
B: Keratin, type II cytoskeletal 5

A: Keratin, type I cytoskeletal 14
B: Keratin, type II cytoskeletal 5


Theoretical massNumber of molelcules
Total (without water)60,7984
Polymers60,7984
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area9840 Å2
ΔGint-125 kcal/mol
Surface area25900 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-57 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.991, 150.991, 141.623
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Keratin, type I cytoskeletal 14 / Cytokeratin-14 / CK-14 / Keratin-14 / K14


Mass: 15326.142 Da / Num. of mol.: 1 / Fragment: UNP residues 295-422
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: 15072.998 Da / Num. of mol.: 1 / Fragment: UNP residues 350-477
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.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 5.11 Å3/Da / Density % sol: 75.93 %
Crystal growTemperature: 293.2 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: K5/K14 2B protein solution (9 mg/mL) was mixed with an equal volume of reservoir solution containing 2.8M NaCl and 0.1M Tris-HCl (pH 8.5). Small crystals formed and were used to seed the ...Details: K5/K14 2B protein solution (9 mg/mL) was mixed with an equal volume of reservoir solution containing 2.8M NaCl and 0.1M Tris-HCl (pH 8.5). Small crystals formed and were used to seed the same mixture of protein solution/reservoir solution, which yielded larger crystals, VAPOR DIFFUSION, HANGING DROP, temperature 293.2K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97944 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 3.005→50 Å / Num. all: 12377 / Num. obs: 12376 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.4_486) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 3.005→40.528 Å / SU ML: 0.35 / σ(F): 0 / Phase error: 27.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 578 4.98 %RANDOM
Rwork0.2091 ---
all0.2103 12532 --
obs0.2103 11603 92.65 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 92.398 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.5727 Å20 Å2-0 Å2
2--10.5727 Å2-0 Å2
3----21.1453 Å2
Refinement stepCycle: LAST / Resolution: 3.005→40.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 0 6 1510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061509
X-RAY DIFFRACTIONf_angle_d0.8212011
X-RAY DIFFRACTIONf_dihedral_angle_d16.04619
X-RAY DIFFRACTIONf_chiral_restr0.051229
X-RAY DIFFRACTIONf_plane_restr0.002265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.005-3.30680.37071170.33272365X-RAY DIFFRACTION80
3.3068-3.7850.27131490.22222742X-RAY DIFFRACTION93
3.785-4.76750.18161530.16242900X-RAY DIFFRACTION98
4.7675-40.5280.23271590.21223018X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 41.6528 Å / Origin y: 36.231 Å / Origin z: 54.8676 Å
111213212223313233
T0.6673 Å20.0748 Å2-0.0187 Å2-0.5084 Å2-0.0021 Å2--0.607 Å2
L0.6281 °20.5071 °20.0264 °2-0.0635 °20.4052 °2--0.2847 °2
S-0.0172 Å °-0.1127 Å °-0.0308 Å °0.1761 Å °-0.0358 Å °0.0166 Å °-0.0879 Å °0.0011 Å °-0 Å °
Refinement TLS groupSelection details: all

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