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HEADER CELL ADHESION, STRUCTURAL PROTEIN 23-DEC-04 1YDI
TITLE HUMAN VINCULIN HEAD DOMAIN (VH1, 1-258) IN COMPLEX WITH HUMAN ALPHA-
TITLE 2 ACTININ'S VINCULIN-BINDING SITE (RESIDUES 731-760)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: VINCULIN ISOFORM VCL;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: ALPHA-ACTININ 4;
COMPND 7 CHAIN: B;
COMPND 8 SYNONYM: NON-MUSCLE ALPHA-ACTININ 4, F-ACTIN CROSS LINKING PROTEIN;
COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET3;
SOURCE 9 MOL_ID: 2;
SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 11 ORGANISM_COMMON: HUMAN;
SOURCE 12 ORGANISM_TAXID: 9606;
SOURCE 13 GENE: ACTN4;
SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS CELL ADHESION, STRUCTURAL PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR T.IZARD
REVDAT 3 14-FEB-24 1YDI 1 SEQADV
REVDAT 2 24-FEB-09 1YDI 1 VERSN
REVDAT 1 19-JUL-05 1YDI 0
JRNL AUTH P.R.BOIS,R.A.BORGON,C.VONRHEIN,T.IZARD
JRNL TITL STRUCTURAL DYNAMICS OF {ALPHA}-ACTININ-VINCULIN
JRNL TITL 2 INTERACTIONS.
JRNL REF MOL.CELL.BIOL. V. 14 6112 2005
JRNL REFN ISSN 0270-7306
JRNL PMID 15988023
JRNL DOI 10.1128/MCB.25.14.6112-6122.2005
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER-TNT
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SMART,VONRHEIN,WOMACK,
REMARK 3 : MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.42
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 92.9
REMARK 3 NUMBER OF REFLECTIONS : 24098
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.181
REMARK 3 R VALUE (WORKING SET) : 0.171
REMARK 3 FREE R VALUE : 0.232
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1192
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 9
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.57
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.66
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 10.30
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL
REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 576
REMARK 3 BIN R VALUE (WORKING SET) : 0.2180
REMARK 3 BIN FREE R VALUE : 0.2735
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 31
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2218
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 466
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 20.20
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.13
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -3.48000
REMARK 3 B22 (A**2) : -1.23000
REMARK 3 B33 (A**2) : 4.72000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.22000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 2291 ; 2.000 ; NULL
REMARK 3 BOND ANGLES : 3094 ; 2.000 ; NULL
REMARK 3 TORSION ANGLES : 1403 ; 0.000 ; NULL
REMARK 3 TRIGONAL CARBON PLANES : 70 ; 2.000 ; NULL
REMARK 3 GENERAL PLANES : 314 ; 5.000 ; NULL
REMARK 3 ISOTROPIC THERMAL FACTORS : 2293 ; 20.000 ; NULL
REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : NULL ; NULL ; NULL
REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : NULL ; NULL ; NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.005
REMARK 3 BOND ANGLES (DEGREES) : 0.89
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : NULL
REMARK 3 OTHER TORSION ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1YDI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-DEC-04.
REMARK 100 THE DEPOSITION ID IS D_1000031404.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : NULL
REMARK 200 RADIATION SOURCE : NULL
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : NULL
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : NULL
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24098
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 40.500
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : NULL
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 43.41
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 27.13400
REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2490 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 15130 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 GLU A 29
REMARK 465 GLY A 30
REMARK 465 GLU A 31
REMARK 465 VAL A 32
REMARK 465 ASP A 33
REMARK 465 GLY A 34
REMARK 465 LYS A 35
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O HOH A 502 O HOH A 588 2.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 NH2 ARG A 72 O GLN A 221 2646 1.96
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1YDI A 1 258 UNP P18206-2 VINC_HUMAN 1 258
DBREF 1YDI B 741 764 UNP O43707 AAC4_HUMAN 734 757
SEQADV 1YDI HIS A -4 UNP P18206-2 EXPRESSION TAG
SEQADV 1YDI HIS A -3 UNP P18206-2 EXPRESSION TAG
SEQADV 1YDI HIS A -2 UNP P18206-2 EXPRESSION TAG
SEQADV 1YDI HIS A -1 UNP P18206-2 EXPRESSION TAG
SEQADV 1YDI HIS A 0 UNP P18206-2 EXPRESSION TAG
SEQRES 1 A 263 HIS HIS HIS HIS HIS MET PRO VAL PHE HIS THR ARG THR
SEQRES 2 A 263 ILE GLU SER ILE LEU GLU PRO VAL ALA GLN GLN ILE SER
SEQRES 3 A 263 HIS LEU VAL ILE MET HIS GLU GLU GLY GLU VAL ASP GLY
SEQRES 4 A 263 LYS ALA ILE PRO ASP LEU THR ALA PRO VAL ALA ALA VAL
SEQRES 5 A 263 GLN ALA ALA VAL SER ASN LEU VAL ARG VAL GLY LYS GLU
SEQRES 6 A 263 THR VAL GLN THR THR GLU ASP GLN ILE LEU LYS ARG ASP
SEQRES 7 A 263 MET PRO PRO ALA PHE ILE LYS VAL GLU ASN ALA CYS THR
SEQRES 8 A 263 LYS LEU VAL GLN ALA ALA GLN MET LEU GLN SER ASP PRO
SEQRES 9 A 263 TYR SER VAL PRO ALA ARG ASP TYR LEU ILE ASP GLY SER
SEQRES 10 A 263 ARG GLY ILE LEU SER GLY THR SER ASP LEU LEU LEU THR
SEQRES 11 A 263 PHE ASP GLU ALA GLU VAL ARG LYS ILE ILE ARG VAL CYS
SEQRES 12 A 263 LYS GLY ILE LEU GLU TYR LEU THR VAL ALA GLU VAL VAL
SEQRES 13 A 263 GLU THR MET GLU ASP LEU VAL THR TYR THR LYS ASN LEU
SEQRES 14 A 263 GLY PRO GLY MET THR LYS MET ALA LYS MET ILE ASP GLU
SEQRES 15 A 263 ARG GLN GLN GLU LEU THR HIS GLN GLU HIS ARG VAL MET
SEQRES 16 A 263 LEU VAL ASN SER MET ASN THR VAL LYS GLU LEU LEU PRO
SEQRES 17 A 263 VAL LEU ILE SER ALA MET LYS ILE PHE VAL THR THR LYS
SEQRES 18 A 263 ASN SER LYS ASN GLN GLY ILE GLU GLU ALA LEU LYS ASN
SEQRES 19 A 263 ARG ASN PHE THR VAL GLU LYS MET SER ALA GLU ILE ASN
SEQRES 20 A 263 GLU ILE ILE ARG VAL LEU GLN LEU THR SER TRP ASP GLU
SEQRES 21 A 263 ASP ALA TRP
SEQRES 1 B 24 VAL GLY TRP GLU GLN LEU LEU THR THR ILE ALA ARG THR
SEQRES 2 B 24 ILE ASN GLU VAL GLU ASN GLN ILE LEU THR ARG
FORMUL 3 HOH *466(H2 O)
HELIX 1 1 THR A 6 MET A 26 1 21
HELIX 2 2 LEU A 40 THR A 65 1 26
HELIX 3 3 ASP A 67 ASP A 98 1 32
HELIX 4 4 SER A 101 ALA A 148 1 48
HELIX 5 5 GLU A 149 VAL A 151 5 3
HELIX 6 6 THR A 153 LEU A 182 1 30
HELIX 7 7 HIS A 184 ASN A 217 1 34
HELIX 8 8 ILE A 223 GLN A 249 1 27
HELIX 9 9 SER A 252 ASP A 256 5 5
HELIX 10 10 GLY B 742 ARG B 764 1 23
CRYST1 42.843 54.268 63.598 90.00 107.57 90.00 P 1 21 1 2
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.023341 0.000000 0.007391 0.00000
SCALE2 0.000000 0.018427 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016493 0.00000
(ATOM LINES ARE NOT SHOWN.)
END