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- PDB-3r6n: Crystal structure of a rigid four spectrin repeat fragment of the... -

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Basic information

Entry
Database: PDB / ID: 3r6n
TitleCrystal structure of a rigid four spectrin repeat fragment of the human desmoplakin plakin domain
ComponentsDesmoplakin
KeywordsCELL ADHESION / spectrin repeat / SH3 domain / desmosome
Function / homology
Function and homology information


bundle of His cell-Purkinje myocyte adhesion involved in cell communication / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / desmosome organization / Keratinization / protein localization to cell-cell junction / ventricular compact myocardium morphogenesis / desmosome / intermediate filament organization / epithelial cell-cell adhesion / intermediate filament cytoskeleton organization ...bundle of His cell-Purkinje myocyte adhesion involved in cell communication / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / desmosome organization / Keratinization / protein localization to cell-cell junction / ventricular compact myocardium morphogenesis / desmosome / intermediate filament organization / epithelial cell-cell adhesion / intermediate filament cytoskeleton organization / Formation of the cornified envelope / peptide cross-linking / fascia adherens / cornified envelope / regulation of ventricular cardiac muscle cell action potential / Apoptotic cleavage of cell adhesion proteins / adherens junction organization / RND1 GTPase cycle / RND3 GTPase cycle / intermediate filament / skin development / regulation of heart rate by cardiac conduction / ficolin-1-rich granule membrane / intercalated disc / epidermis development / keratinocyte differentiation / protein kinase C binding / adherens junction / wound healing / structural constituent of cytoskeleton / cell-cell adhesion / scaffold protein binding / basolateral plasma membrane / Neutrophil degranulation / structural molecule activity / RNA binding / extracellular exosome / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1060 / Spectrin-like repeat / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / SH3 domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1060 / Spectrin-like repeat / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / SH3 domain / Plectin repeat / Plakin / Spectrin/alpha-actinin / Spectrin repeats / SH3 Domains / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / SH3 type barrels. / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
(4S,5S)-1,2-DITHIANE-4,5-DIOL / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Desmoplakin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.95 Å
AuthorsChoi, H.-J. / Weis, W.I.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal structure of a rigid four-spectrin-repeat fragment of the human desmoplakin plakin domain.
Authors: Choi, H.J. / Weis, W.I.
History
DepositionMar 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Desmoplakin
B: Desmoplakin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,1966
Polymers106,5832
Non-polymers6134
Water00
1
A: Desmoplakin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5983
Polymers53,2921
Non-polymers3062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Desmoplakin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5983
Polymers53,2921
Non-polymers3062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)157.520, 82.520, 139.980
Angle α, β, γ (deg.)90.000, 125.540, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Desmoplakin / DP / 250/210 kDa paraneoplastic pemphigus antigen


Mass: 53291.738 Da / Num. of mol.: 2 / Fragment: Plakin domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DSP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P15924
#2: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2S2
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2

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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: 3.47 Å3/Da / Density % sol: 64.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 16% PEG 8000, 0.1M Tris-Cl (pH 8.5), 4mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.946→45.691 Å / Num. all: 30845 / Num. obs: 30845 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 16.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.95-3.032.60.3652574821870.36596.7
3.03-3.1130.2832.6662322270.283100
3.11-3.230.2123.5649121810.212100
3.2-3.330.1734.2624920980.173100
3.3-3.4130.1265.8604920350.126100
3.41-3.5330.0987.4578819520.098100
3.53-3.6630.0798.9566919110.079100
3.66-3.8130.06710.6546118420.067100
3.81-3.9830.05812.1514617280.058100
3.98-4.1730.05412.6506417050.054100
4.17-4.42.90.04714.2475316120.047100
4.4-4.6630.04115.9454115270.04199.9
4.66-4.9930.03716.5414714030.03799.8
4.99-5.3930.03815.8389413190.03899.9
5.39-5.930.04413.5369812490.04499.8
5.9-6.62.90.04114.4317110870.04199.4
6.6-7.622.90.03616.4294510010.03699.5
7.62-9.332.90.03315.523988260.03398.9
9.33-13.192.90.02821.518016260.02897
13.19-56.982.80.03318.39103290.03388.2

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
PHASERphasing
SnBphasing
RESOLVEphasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.95→45.653 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.78 / SU ML: 0.38 / σ(F): 1.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 3090 10.04 %RANDOM
Rwork0.2164 ---
obs0.2212 30776 99.31 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.143 Å2 / ksol: 0.283 e/Å3
Displacement parametersBiso max: 202.25 Å2 / Biso mean: 105.199 Å2 / Biso min: 46.44 Å2
Baniso -1Baniso -2Baniso -3
1-6.1791 Å2-0 Å2-10.1428 Å2
2--0.7438 Å2-0 Å2
3----6.9229 Å2
Refinement stepCycle: LAST / Resolution: 2.95→45.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7454 0 32 0 7486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037632
X-RAY DIFFRACTIONf_angle_d0.5910281
X-RAY DIFFRACTIONf_chiral_restr0.0431102
X-RAY DIFFRACTIONf_plane_restr0.0021320
X-RAY DIFFRACTIONf_dihedral_angle_d14.8332965
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-2.99610.35231210.35161179130095
2.9961-3.04520.31991210.321312941415100
3.0452-3.09770.38981510.317112191370100
3.0977-3.1540.37281530.3112541407100
3.154-3.21470.30531390.296712521391100
3.2147-3.28030.38151430.287312831426100
3.2803-3.35160.29471520.283912321384100
3.3516-3.42950.33291360.273112691405100
3.4295-3.51520.3081320.259612721404100
3.5152-3.61030.27241550.254512301385100
3.6103-3.71640.3051470.239812711418100
3.7164-3.83630.28451370.252512371374100
3.8363-3.97340.32451320.235812781410100
3.9734-4.13240.2811500.227412641414100
4.1324-4.32030.27081510.208712711422100
4.3203-4.54790.2521420.183112511393100
4.5479-4.83250.22881420.181912701412100
4.8325-5.20520.24571320.17812831415100
5.2052-5.72810.28711200.232712851405100
5.7281-6.55490.28581500.25321265141599
6.5549-8.25050.24921440.18021282142699
8.2505-45.65820.17061400.14671245138594
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)
10.6399-0.32740.4857-0.0228-1.46777.0559-0.07430.14030.18610.038-0.017-0.0089-0.44450.09840.03510.7875-0.1578-0.04780.52460.15650.7009-26.996927.9597-78.7457
20.08740.0134-0.5644-0.01871.18465.5756-0.0123-0.42650.0664-0.23080.1861-0.165-0.74460.6759-0.23440.7312-0.0281-0.00921.1667-0.05730.7681-23.639623.9283-10.0034
31.37230.321-0.03242.45941.60514.6929-0.02230.1261-0.0254-0.03180.03550.19750.4059-0.54420.0510.5116-0.03150.0120.70140.10380.6377-28.178710.6695-40.4637
42.1599-0.86720.3218-0.0851-0.29511.7522-0.4069-0.7061-0.05950.21440.5060.00890.39730.6833-0.02961.10870.22070.03371.1453-0.01580.6767-33.359625.013326.0571
50.9939-1.6362-0.07756.44492.05621.4373-0.0508-0.2774-0.0073-0.116-0.09210.55590.1503-0.25070.11060.57980.0483-0.03250.7168-0.11210.76828.6959-15.2486-45.3467
60.9806-1.55270.29442.24311.6631.11810.49320.2717-0.0699-0.4426-0.1325-0.68170.03080.0523-0.11620.79190.07130.09431.0411-0.11361.1538-11.421949.7123-31.6638
71.1706-1.02350.44293.1625-0.42571.006-0.0940.0521-0.16260.9273-0.1014-0.2820.1127-0.0164-0.02561.06150.269-0.20551.0372-0.35191.22720.566119.44-22.7671
82.1898-1.11510.33070.5949-1.02451.5486-0.0864-0.26740.32280.32430.1819-0.1214-0.47570.0241-0.04171.04120.10310.06570.68930.02820.7863-32.546177.2884-20.7872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 178:379A178 - 379
2X-RAY DIFFRACTION2chain A and resid 380:459A380 - 459
3X-RAY DIFFRACTION3chain A and resid 460:529A460 - 529
4X-RAY DIFFRACTION4chain A and resid 530:627A530 - 627
5X-RAY DIFFRACTION5chain B and resid 179:379B179 - 379
6X-RAY DIFFRACTION6chain B and resid 380:459B380 - 459
7X-RAY DIFFRACTION7chain B and resid 460:529B460 - 529
8X-RAY DIFFRACTION8chain B and resid 530:625B530 - 625

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