1NYP - Header Asymmetric Unit

HEADER CELL ADHESION 13-FEB-03 1NYP

TITLE 4TH LIM DOMAIN OF PINCH PROTEIN

COMPND MOL_ID: 1; COMPND 2 MOLECULE: PINCH PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 4TH LIM DOMAIN; COMPND 5 SYNONYM: LIM AND SENESCENT CELL ANTIGEN-LIKE DOMAINS 1; COMPND 6 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: LIMS1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-4T1

KEYWDS LIM DOMAIN, PROTEIN RECOGNITION, CELL ADHESION

EXPDTA SOLUTION NMR

NUMMDL 20

AUTHOR A.VELYVIS,J.VAYNBERG,O.VINOGRADOVA,Y.ZHANG,C.WU,J.QIN

REVDAT 2 24-FEB-09 1NYP 1 VERSN REVDAT 1 01-JUL-03 1NYP 0

JRNL AUTH A.VELYVIS,J.VAYNBERG,Y.YANG,O.VINOGRADOVA,Y.ZHANG, JRNL AUTH 2 C.WU,J.QIN JRNL TITL STRUCTURAL AND FUNCTIONAL INSIGHTS INTO PINCH LIM4 JRNL TITL 2 DOMAIN-MEDIATED INTEGRIN SIGNALING JRNL REF NAT.STRUCT.BIOL. V. 10 558 2003 JRNL REFN ISSN 1072-8368 JRNL PMID 12794636 JRNL DOI 10.1038/NSB938

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SA PROTOCOL WITHOUT ZN COFACTORS REMARK 3 STARTING FROM LINEAR PROTEIN STRUCTURE, FOLLOWED BY ADDITION REMARK 3 OF ZN INTO STRUCTURES AND MINIMIZATION

REMARK 4 REMARK 4 1NYP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-03. REMARK 100 THE RCSB ID CODE IS RCSB018358.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.13 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.7 MM U-15N,13C-LIM4; 95% REMARK 210 H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D-15N,13C-EDITED-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, PIPP, X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL

REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS.

REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 MET A 3 167.87 -49.80 REMARK 500 1 GLU A 16 61.47 -160.54 REMARK 500 1 MET A 23 17.19 58.09 REMARK 500 1 LYS A 25 -154.80 -130.23 REMARK 500 1 LYS A 36 -31.69 -138.81 REMARK 500 1 GLU A 38 47.60 71.70 REMARK 500 1 PHE A 41 56.90 -95.78 REMARK 500 1 CYS A 55 177.47 -57.55 REMARK 500 1 PHE A 63 -81.64 -158.58 REMARK 500 2 VAL A 5 117.70 57.16 REMARK 500 2 GLU A 16 62.84 -161.77 REMARK 500 2 MET A 23 16.01 58.38 REMARK 500 2 LYS A 25 -151.11 -133.05 REMARK 500 2 ALA A 35 35.11 -92.46 REMARK 500 2 LYS A 36 -40.23 -142.99 REMARK 500 2 GLU A 38 47.89 75.10 REMARK 500 2 PHE A 41 57.82 -96.21 REMARK 500 2 CYS A 55 175.80 -57.28 REMARK 500 2 PHE A 63 -81.54 -158.49 REMARK 500 2 ASP A 65 80.97 55.92 REMARK 500 3 MET A 3 -167.53 -163.93 REMARK 500 3 GLU A 16 62.02 -159.59 REMARK 500 3 MET A 23 16.96 57.52 REMARK 500 3 LYS A 25 -155.37 -125.38 REMARK 500 3 LYS A 36 -32.03 -138.70 REMARK 500 3 PHE A 41 56.44 -95.78 REMARK 500 3 CYS A 55 178.15 -57.81 REMARK 500 3 PHE A 63 -81.93 -160.13 REMARK 500 3 ASP A 65 25.27 -172.55 REMARK 500 4 SER A 2 43.49 -166.43 REMARK 500 4 MET A 3 -128.48 50.62 REMARK 500 4 VAL A 5 129.27 57.13 REMARK 500 4 GLU A 16 62.12 -159.19 REMARK 500 4 MET A 23 18.14 58.10 REMARK 500 4 LYS A 25 -154.67 -130.32 REMARK 500 4 LYS A 36 -39.07 -134.10 REMARK 500 4 GLU A 38 46.94 73.70 REMARK 500 4 LYS A 50 20.94 44.73 REMARK 500 4 CYS A 55 172.03 -56.57 REMARK 500 4 PHE A 63 -83.88 -156.11 REMARK 500 4 ASP A 65 81.46 56.38 REMARK 500 5 SER A 2 -120.49 -165.90 REMARK 500 5 MET A 3 98.56 51.63 REMARK 500 5 VAL A 5 116.19 56.67 REMARK 500 5 GLU A 16 62.41 -161.26 REMARK 500 5 MET A 23 14.46 58.31 REMARK 500 5 LYS A 25 -154.83 -120.21 REMARK 500 5 LYS A 36 -33.21 -138.09 REMARK 500 5 PHE A 41 56.35 -96.08 REMARK 500 5 LYS A 50 21.66 42.33 REMARK 500 5 CYS A 55 -175.51 -56.51 REMARK 500 5 PHE A 63 -83.31 -153.79 REMARK 500 5 ASP A 65 -24.17 170.27 REMARK 500 6 MET A 3 40.31 -164.36 REMARK 500 6 GLU A 16 61.25 -160.45 REMARK 500 6 MET A 23 16.80 58.07 REMARK 500 6 LYS A 25 -154.78 -130.72 REMARK 500 6 LYS A 36 -32.75 -135.43 REMARK 500 6 PHE A 41 56.81 -95.72 REMARK 500 6 LYS A 50 21.51 42.04 REMARK 500 6 CYS A 55 178.76 -56.56 REMARK 500 6 PHE A 63 -81.71 -153.74 REMARK 500 6 ASP A 65 -18.43 158.79 REMARK 500 7 SER A 2 102.87 55.50 REMARK 500 7 MET A 3 31.16 -74.22 REMARK 500 7 GLU A 16 62.40 -158.38 REMARK 500 7 MET A 23 16.65 58.31 REMARK 500 7 LYS A 25 -153.83 -130.83 REMARK 500 7 LYS A 36 -31.53 -136.02 REMARK 500 7 GLU A 38 47.43 71.98 REMARK 500 7 PHE A 41 57.82 -95.50 REMARK 500 7 HIS A 44 -163.61 -115.64 REMARK 500 7 LYS A 50 22.41 41.80 REMARK 500 7 CYS A 55 179.15 -56.05 REMARK 500 7 PHE A 63 -83.48 -156.85 REMARK 500 7 ASP A 65 71.16 49.78 REMARK 500 8 GLU A 16 61.45 -161.38 REMARK 500 8 MET A 23 15.98 58.02 REMARK 500 8 LYS A 25 -154.69 -124.24 REMARK 500 8 ALA A 35 34.49 -92.25 REMARK 500 8 LYS A 36 -40.05 -142.79 REMARK 500 8 GLU A 38 47.59 76.32 REMARK 500 8 PHE A 41 58.13 -96.11 REMARK 500 8 CYS A 55 173.27 -56.05 REMARK 500 8 PHE A 63 -80.16 -160.33 REMARK 500 8 ASP A 65 -99.18 -164.40 REMARK 500 9 SER A 2 -64.27 -159.37 REMARK 500 9 VAL A 5 128.98 57.25 REMARK 500 9 GLU A 16 70.39 -170.30 REMARK 500 9 MET A 23 18.40 57.65 REMARK 500 9 LYS A 25 -156.19 -129.37 REMARK 500 9 GLU A 38 46.56 71.51 REMARK 500 9 PHE A 41 59.46 -93.01 REMARK 500 9 CYS A 55 173.92 -57.40 REMARK 500 9 PHE A 63 -85.11 -154.30 REMARK 500 10 SER A 2 98.35 53.34 REMARK 500 10 MET A 3 -138.69 -62.45 REMARK 500 10 VAL A 5 129.80 57.28 REMARK 500 10 GLU A 16 59.38 -159.21 REMARK 500 10 MET A 23 16.39 57.52 REMARK 500 10 LYS A 25 -154.67 -125.75 REMARK 500 10 ALA A 35 30.48 -91.50 REMARK 500 10 LYS A 36 -31.01 -139.65 REMARK 500 10 GLU A 38 45.89 74.38 REMARK 500 10 PHE A 41 55.69 -93.28 REMARK 500 10 HIS A 44 -164.52 -115.69 REMARK 500 10 PHE A 63 -79.44 -160.37 REMARK 500 11 SER A 2 85.19 52.12 REMARK 500 11 GLU A 16 69.06 -167.73 REMARK 500 11 MET A 23 17.77 57.84 REMARK 500 11 LYS A 25 -156.06 -124.25 REMARK 500 11 LYS A 36 -42.04 -134.21 REMARK 500 11 GLU A 38 47.54 72.68 REMARK 500 11 PHE A 41 59.97 -95.46 REMARK 500 11 LYS A 50 24.75 42.39 REMARK 500 11 CYS A 55 174.02 -59.38 REMARK 500 11 PHE A 63 -83.36 -160.14 REMARK 500 12 GLU A 16 67.96 -166.30 REMARK 500 12 MET A 23 16.26 58.34 REMARK 500 12 LYS A 25 -154.56 -130.56 REMARK 500 12 LYS A 36 -31.29 -139.80 REMARK 500 12 PHE A 41 57.85 -95.93 REMARK 500 12 HIS A 44 -158.51 -114.36 REMARK 500 12 CYS A 55 178.31 -56.85 REMARK 500 12 PHE A 63 -84.06 -158.60 REMARK 500 13 SER A 2 -173.87 -173.94 REMARK 500 13 GLU A 16 61.68 -160.73 REMARK 500 13 MET A 23 17.02 58.74 REMARK 500 13 LYS A 25 -154.41 -133.89 REMARK 500 13 LYS A 36 -30.68 -132.63 REMARK 500 13 CYS A 55 174.67 -57.22 REMARK 500 13 PHE A 63 -84.91 -154.74 REMARK 500 13 ASP A 65 88.65 -173.11 REMARK 500 14 SER A 2 -157.50 -65.06 REMARK 500 14 VAL A 5 122.87 57.50 REMARK 500 14 GLU A 16 61.92 -160.73 REMARK 500 14 MET A 23 14.52 58.74 REMARK 500 14 LYS A 25 -154.36 -125.08 REMARK 500 14 ALA A 35 32.03 -91.22 REMARK 500 14 LYS A 36 -41.55 -140.25 REMARK 500 14 GLU A 38 48.04 75.51 REMARK 500 14 PHE A 41 56.98 -96.14 REMARK 500 14 HIS A 44 -163.27 -115.23 REMARK 500 14 CYS A 55 -179.82 -56.80 REMARK 500 14 PHE A 63 -81.06 -158.52 REMARK 500 15 SER A 2 96.71 -170.22 REMARK 500 15 MET A 3 75.51 -63.97 REMARK 500 15 VAL A 5 116.22 57.09 REMARK 500 15 GLU A 16 59.73 -159.38 REMARK 500 15 MET A 23 16.39 58.26 REMARK 500 15 LYS A 25 -154.45 -135.86 REMARK 500 15 LYS A 36 -32.15 -135.83 REMARK 500 15 LYS A 50 25.40 37.45 REMARK 500 15 CYS A 55 178.43 -56.16 REMARK 500 15 PHE A 63 -84.17 -152.78 REMARK 500 15 ASP A 65 -92.10 168.40 REMARK 500 16 SER A 2 42.23 -175.28 REMARK 500 16 GLU A 16 61.38 -161.29 REMARK 500 16 MET A 23 16.83 58.79 REMARK 500 16 LYS A 25 -154.47 -131.71 REMARK 500 16 LYS A 36 -33.43 -134.19 REMARK 500 16 GLU A 38 46.50 76.22 REMARK 500 16 PHE A 41 57.86 -95.93 REMARK 500 16 CYS A 55 176.75 -57.61 REMARK 500 16 PHE A 63 -80.46 -158.59 REMARK 500 17 SER A 2 6.41 -173.07 REMARK 500 17 MET A 3 63.98 -152.73 REMARK 500 17 GLU A 16 69.88 -169.25 REMARK 500 17 MET A 23 19.36 58.02 REMARK 500 17 LYS A 25 -156.76 -118.95 REMARK 500 17 LYS A 36 -31.34 -135.44 REMARK 500 17 GLU A 38 47.58 72.75 REMARK 500 17 PHE A 41 57.93 -96.05 REMARK 500 17 CYS A 55 176.58 -58.00 REMARK 500 17 PHE A 63 -87.61 -155.34 REMARK 500 17 ASP A 65 89.51 -173.43 REMARK 500 18 MET A 3 67.27 -176.17 REMARK 500 18 VAL A 5 119.71 57.21 REMARK 500 18 GLU A 16 69.18 -168.62 REMARK 500 18 MET A 23 14.71 57.50 REMARK 500 18 LYS A 25 -155.55 -115.24 REMARK 500 18 LYS A 36 -31.07 -137.80 REMARK 500 18 GLU A 38 48.18 72.20 REMARK 500 18 PHE A 41 58.07 -95.90 REMARK 500 18 HIS A 44 -163.82 -115.85 REMARK 500 18 LYS A 50 23.12 45.15 REMARK 500 18 CYS A 55 -179.47 -56.12 REMARK 500 18 PHE A 63 -86.50 -162.59 REMARK 500 19 SER A 2 115.45 -178.95 REMARK 500 19 MET A 3 -128.07 -64.11 REMARK 500 19 VAL A 5 117.06 57.18 REMARK 500 19 GLU A 16 63.57 -161.33 REMARK 500 19 MET A 23 17.52 58.16 REMARK 500 19 LYS A 25 -155.96 -120.37 REMARK 500 19 LYS A 36 -32.06 -138.87 REMARK 500 19 GLU A 38 47.31 73.43 REMARK 500 19 PHE A 41 58.83 -96.34 REMARK 500 19 CYS A 55 175.04 -57.36 REMARK 500 19 PHE A 63 -81.82 -155.03 REMARK 500 19 ASP A 65 79.57 52.10 REMARK 500 20 SER A 2 -16.52 -165.50 REMARK 500 20 MET A 3 -176.44 -56.28 REMARK 500 20 GLU A 16 62.73 -160.91 REMARK 500 20 MET A 23 16.44 58.12 REMARK 500 20 LYS A 25 -153.97 -123.44 REMARK 500 20 LYS A 36 -31.68 -138.55 REMARK 500 20 GLU A 38 47.28 75.26 REMARK 500 20 PHE A 41 58.46 -96.15 REMARK 500 20 CYS A 55 176.70 -57.34 REMARK 500 20 PHE A 63 -83.59 -160.08 REMARK 500 20 ASP A 65 -93.94 -179.43 REMARK 500 REMARK 500 REMARK: NULL

REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 67 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 8 SG REMARK 620 2 HIS A 31 ND1 123.1 REMARK 620 3 CYS A 11 SG 109.6 106.4 REMARK 620 4 HIS A 28 ND1 104.8 104.1 108.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 68 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 37 SG REMARK 620 2 CYS A 34 SG 104.5 REMARK 620 3 CYS A 55 SG 92.2 117.0 REMARK 620 4 HIS A 58 ND1 97.0 117.7 119.8 REMARK 620 N 1 2 3

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 67 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 68

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G47 RELATED DB: PDB REMARK 900 ANOTHER LIM DOMAIN FROM THE SAME MULTI-DOMAIN ADAPTOR REMARK 900 PROTEIN

DBREF 1NYP A 3 66 UNP P48059 PINC_HUMAN 188 251

SEQADV 1NYP GLY A 1 UNP P48059 CLONING ARTIFACT SEQADV 1NYP SER A 2 UNP P48059 CLONING ARTIFACT

SEQRES 1 A 66 GLY SER MET GLY VAL PRO ILE CYS GLY ALA CYS ARG ARG SEQRES 2 A 66 PRO ILE GLU GLY ARG VAL VAL ASN ALA MET GLY LYS GLN SEQRES 3 A 66 TRP HIS VAL GLU HIS PHE VAL CYS ALA LYS CYS GLU LYS SEQRES 4 A 66 PRO PHE LEU GLY HIS ARG HIS TYR GLU ARG LYS GLY LEU SEQRES 5 A 66 ALA TYR CYS GLU THR HIS TYR ASN GLN LEU PHE GLY ASP SEQRES 6 A 66 VAL

HET ZN A 67 1 HET ZN A 68 1

HETNAM ZN ZINC ION

FORMUL 2 ZN 2(ZN 2+)

HELIX 1 1 CYS A 55 PHE A 63 1 9

SHEET 1 A 2 ILE A 7 CYS A 8 0 SHEET 2 A 2 ARG A 13 PRO A 14 -1 O ARG A 13 N CYS A 8 SHEET 1 B 2 VAL A 19 VAL A 20 0 SHEET 2 B 2 TRP A 27 HIS A 28 -1 O TRP A 27 N VAL A 20 SHEET 1 C 2 TYR A 47 ARG A 49 0 SHEET 2 C 2 LEU A 52 TYR A 54 -1 O TYR A 54 N TYR A 47

LINK ZN ZN A 67 SG CYS A 8 1555 1555 2.30 LINK ZN ZN A 67 ND1 HIS A 31 1555 1555 2.00 LINK ZN ZN A 67 SG CYS A 11 1555 1555 2.30 LINK ZN ZN A 67 ND1 HIS A 28 1555 1555 2.00 LINK ZN ZN A 68 SG CYS A 37 1555 1555 2.30 LINK ZN ZN A 68 SG CYS A 34 1555 1555 2.30 LINK ZN ZN A 68 SG CYS A 55 1555 1555 2.30 LINK ZN ZN A 68 ND1 HIS A 58 1555 1555 2.00

SITE 1 AC1 4 CYS A 8 CYS A 11 HIS A 28 HIS A 31 SITE 1 AC2 4 CYS A 34 CYS A 37 CYS A 55 HIS A 58

CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1

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 1.000000 0.000000 0.000000 0.00000

SCALE2 0.000000 1.000000 0.000000 0.00000

SCALE3 0.000000 0.000000 1.000000 0.00000