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- PDB-4cai: Structure of inner DysF domain of human dysferlin -

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Basic information

Entry
Database: PDB / ID: 4cai
TitleStructure of inner DysF domain of human dysferlin
ComponentsDYSFERLIN
KeywordsMEMBRANE PROTEIN / MEMBRANE REPAIR / LIMB-GIRDLE MUSCULAR DYSTROPHY / DYSF DOMAIN
Function / homology
Function and homology information


monocyte activation involved in immune response / regulation of neurotransmitter secretion / calcium-dependent phospholipid binding / macrophage activation involved in immune response / negative regulation of phagocytosis / endocytic vesicle / Smooth Muscle Contraction / T-tubule / cytoplasmic vesicle membrane / sarcolemma ...monocyte activation involved in immune response / regulation of neurotransmitter secretion / calcium-dependent phospholipid binding / macrophage activation involved in immune response / negative regulation of phagocytosis / endocytic vesicle / Smooth Muscle Contraction / T-tubule / cytoplasmic vesicle membrane / sarcolemma / phospholipid binding / centriolar satellite / synaptic vesicle membrane / late endosome / early endosome / endosome / calcium ion binding / extracellular exosome / plasma membrane
Similarity search - Function
Ferlin A-domain / FerA (NUC095) domain / FerA / Peroxin/Ferlin domain / Dysferlin domain, N-terminal region. / Dysferlin domain, C-terminal region. / Ferlin B-domain / FerIin domain / Ferlin, C-terminal domain / Ferlin, second C2 domain ...Ferlin A-domain / FerA (NUC095) domain / FerA / Peroxin/Ferlin domain / Dysferlin domain, N-terminal region. / Dysferlin domain, C-terminal region. / Ferlin B-domain / FerIin domain / Ferlin, C-terminal domain / Ferlin, second C2 domain / Ferlin family / Ferlin, third C2 domain / Ferlin, fourth C2 domain / Ferlin, fifth C2 domain / Ferlin, sixth C2 domain / Ferlin, first C2 domain / : / FerB (NUC096) domain / FerI (NUC094) domain / Ferlin C-terminus / Ferlin dsRNA-binding domain-like domain / FerB / FerI / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Dysferlin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSula, A. / Cole, A.R. / Yeats, C. / Orengo, C. / Keep, N.H.
Citation
Journal: Bmc Struct.Biol. / Year: 2014
Title: Crystal Structures of the Human Dysferlin Inner Dysf Domain
Authors: Sula, A. / Cole, A.R. / Yeats, C. / Orengo, C. / Keep, N.H.
#1: Journal: J.Mol.Biol. / Year: 2008
Title: Solution Structure of the Inner Dysf Domain of Myoferlin and Implications for Limb Girdle Muscular Dystrophy Type 2B.
Authors: Patel, P. / Harris, R. / Geddes, S.M. / Strehle, E. / Watson, J.D. / Bashir, R. / Bushby, K. / Driscoll, P.C. / Keep, N.H.
History
DepositionOct 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: DYSFERLIN
B: DYSFERLIN
C: DYSFERLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0946
Polymers40,8093
Non-polymers2853
Water1,72996
1
A: DYSFERLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6982
Polymers13,6031
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DYSFERLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6982
Polymers13,6031
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DYSFERLIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6982
Polymers13,6031
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-27.9 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.894, 77.473, 74.504
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.014, -0.997, -0.07), (-0.021, 0.07, -0.997), (1, -0.012, -0.022)-39.166, 0.179, 39.758
2given(0.022, -0.047, 0.999), (-1, 0.013, 0.023), (-0.014, -0.999, -0.047)-40.29, -40.684, -0.218

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Components

#1: Protein DYSFERLIN / DYSTROPHY-ASSOCIATED FER-1-LIKE PROTEIN / FER-1-LIKE PROTEIN 1


Mass: 13603.146 Da / Num. of mol.: 3 / Fragment: INNER DYSF DOMAIN, RESIDUES 942-1052
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: MUSCLE / Description: CDNA PROVIDED BY JAIN FOUNDATION / Plasmid: PNIC28BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: O75923
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.85 Å3/Da / Density % sol: 56.8 % / Description: NONE
Crystal growpH: 7.5
Details: 0.04M SODIUM DIHYDROGEN PHOSPHATE, 16% PEG 8000, 20% GLYCEROL, 0.2M NABR, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.03753
DetectorType: PILATUS / Date: Sep 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03753 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 24062 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 45.68 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.4
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CAH

4cah


Resolution: 2.2→35.505 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2271 1206 5 %
Rwork0.1858 --
obs0.188 24002 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→35.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2808 0 15 96 2919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112972
X-RAY DIFFRACTIONf_angle_d1.3584050
X-RAY DIFFRACTIONf_dihedral_angle_d13.6181136
X-RAY DIFFRACTIONf_chiral_restr0.076387
X-RAY DIFFRACTIONf_plane_restr0.007528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.28810.31021220.24572510X-RAY DIFFRACTION100
2.2881-2.39220.31611230.23472498X-RAY DIFFRACTION100
2.3922-2.51830.26741380.2332496X-RAY DIFFRACTION100
2.5183-2.67610.3311560.24042491X-RAY DIFFRACTION100
2.6761-2.88260.27251210.22062500X-RAY DIFFRACTION99
2.8826-3.17250.29681250.20362532X-RAY DIFFRACTION99
3.1725-3.63120.21031490.1672521X-RAY DIFFRACTION100
3.6312-4.57340.17291360.15422564X-RAY DIFFRACTION100
4.5734-35.50960.20451360.1792684X-RAY DIFFRACTION99
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)
14.19-2.8506-5.52757.43215.34286.9443-0.0897-0.452-0.17550.17450.17770.09740.2740.13790.07080.3210.057-0.01160.45150.00440.519-32.532-25.025519.2493
25.22323.16513.29627.4449-1.86534.6902-1.5724-1.8713-1.35212.34640.44850.53960.1841-1.26371.00741.01620.26280.49620.95020.12841.1067-49.0781-13.166935.798
31.9505-2.6174-1.45176.8579-2.40448.7986-0.14130.039-1.08980.3148-0.44741.67360.7684-0.74810.36550.571-0.20890.04050.673-0.0791.2152-43.3403-25.610324.6353
44.7742-2.6097-1.73678.74846.6777.5079-0.1011-0.3506-0.26150.56080.05710.28220.7228-0.05760.020.2358-0.0342-0.0460.2860.03040.4132-29.4554-26.625522.9557
52.5523-1.4235-3.92177.9653-2.76189.43010.0631-0.04990.1672-0.7291-0.08971.3560.0997-0.5736-0.03440.43910.0267-0.08760.4184-0.14810.89-45.7859-10.783824.0404
65.1041-4.8035-3.73265.41723.14793.3935-0.0767-0.15410.15110.24930.05350.4893-0.0028-0.17280.1030.3935-0.01150.00590.4176-0.08270.7124-37.6025-16.67123.6753
74.9956.05-5.04075.0933-4.48716.23310.2034-0.28310.50640.389-0.03130.6339-0.1942-0.1379-0.17230.36280.0323-0.00110.39350.00280.4128-19.9726-8.201825.3866
84.9667-2.61473.23945.07543.3069.37091.2978-0.25260.40040.6643-1.8791-0.8187-0.8331.22930.27410.6407-0.32020.07790.59420.09020.7656-3.97558.882914.5081
94.78863.2561-0.88972.2944-0.70243.83361.0954-0.75642.67530.9246-0.98582.0192-2.53150.2903-0.04231.1542-0.09220.1240.7043-0.28261.0738-15.83514.602923.8265
106.35913.4569-5.04316.02611.3198.04511.1624-2.85780.06121.8605-1.27480.1531-1.72081.80350.21750.9168-0.3239-0.06520.7563-0.25030.2827-12.2409-1.2129.8521
117.47032.7189-5.36323.3623-3.13964.16420.1244-1.0225-0.07190.2314-0.1273-0.24050.22350.77540.02560.28220.0556-0.02670.3195-0.02810.2778-16.1391-12.208628.6131
129.07165.8515-5.1214.6287-4.14895.07670.3742-0.89120.11970.537-0.59870.3685-0.50130.3810.23370.35510.00410.03070.2877-0.08690.2778-18.103-8.74924.9506
134.22815.44193.87768.47698.34965.57630.0130.2928-0.1933-0.2639-0.1229-0.0432-0.0780.17370.14560.3484-0.022-0.03450.4325-0.06330.4331-15.5158-19.63327.2285
142.9399-2.45230.93495.1574-4.98885.82670.31681.3366-1.4681-0.22330.0060.6282.65931.627-0.97340.55230.0728-0.14950.7885-0.52230.9404-27.612-35.1284-9.4538
159.0059-2.96791.83239.8029-1.47752.4373-0.02670.480.7415-0.4780.13220.2498-0.2568-0.2913-0.08280.3942-0.0361-0.05350.5564-0.06510.4369-33.4292-23.7459-8.038
168.02053.83465.51814.43954.78678.69440.17950.1199-0.29430.13280.11-0.2291-0.04260.0757-0.29480.257-0.00190.02010.2967-0.04730.3975-15.7768-21.53147.7473
176.97172.00471.60582.7539-2.49645.3375-0.05580.37940.0035-0.42790.0624-0.5491-0.2651-0.29990.01950.3861-0.0047-0.02220.3103-0.02830.2446-14.18571.234210.4598
187.29572.55384.98812.1907-0.08186.7666-0.3010.08360.94710.2890.1260.0419-1.032-0.3050.19040.55730.00460.02960.25530.00750.4019-15.05557.93698.9731
192.2032-1.5289-2.49258.98788.73559.6495-0.5524-1.31122.0862-1.55560.85880.77040.25910.8229-0.45790.6092-0.0358-0.06030.5830.08770.6086-33.449-19.7443-15.4063
207.09152.14661.19152.86481.33735.41630.1008-0.0952-0.40660.2846-0.2213-0.25050.0045-0.28140.06220.2889-0.0224-0.02270.2922-0.04930.4079-26.0766-27.07086.2875
214.4331-3.68553.51436.7274-2.27383.8889-0.18831.4246-0.8115-0.24770.71720.0989-1.24750.8537-0.46990.5684-0.13750.17910.9264-0.12370.6285-15.4697-24.298-3.9042
224.75154.4958-0.33294.8407-1.33173.2032-0.22850.5056-1.2810.03470.6649-1.19090.3880.7252-0.41360.33260.04280.0290.4618-0.1150.6004-5.7569-20.83189.7774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 943 THROUGH 958 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 959 THROUGH 968 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 969 THROUGH 985 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 986 THROUGH 1005 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 1006 THROUGH 1025 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 1026 THROUGH 1051 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 943 THROUGH 958 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 959 THROUGH 968 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 969 THROUGH 978 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 979 THROUGH 986 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 987 THROUGH 1003)
12X-RAY DIFFRACTION12CHAIN B AND (RESID 1037 THROUGH 1051 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 943 THROUGH 958 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 959 THROUGH 968)
15X-RAY DIFFRACTION15CHAIN C AND (RESID 1021 THROUGH 1036 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 1037 THROUGH 1051 )
17X-RAY DIFFRACTION17CHAIN B AND (RESID 1004 THROUGH 1020)
18X-RAY DIFFRACTION18CHAIN B AND (RESID 1021 THROUGH 1036)
19X-RAY DIFFRACTION19CHAIN C AND (RESID 1016 THROUGH 1020)
20X-RAY DIFFRACTION20CHAIN C AND (RESID 996 THROUGH 1015 )
21X-RAY DIFFRACTION21CHAIN C AND (RESID 969 THROUGH 985 )
22X-RAY DIFFRACTION22CHAIN C AND (RESID 986 THROUGH 995 )

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