HEADER CELL ADHESION 06-NOV-20 7KNV TITLE SOLUTION NMR STRUCTURE OF CDHR3 EXTRACELLULAR DOMAIN EC1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CADHERIN-RELATED FAMILY MEMBER 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN EC1, RESIDUES 21-130; COMPND 5 SYNONYM: CADHERIN-LIKE PROTEIN 28; 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: CDHR3, CDH28; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RECEPTOR, CELL ADHESION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR W.LEE,M.TONELLI,R.O.FREDERICK,K.E.WATTERS,J.L.MARKLEY,A.C.PALMENBERG REVDAT 2 14-JUN-23 7KNV 1 JRNL REVDAT 1 03-FEB-21 7KNV 0 JRNL AUTH W.LEE,R.O.FREDERICK,M.TONELLI,A.C.PALMENBERG JRNL TITL SOLUTION NMR DETERMINATION OF THE CDHR3 RHINOVIRUS-C BINDING JRNL TITL 2 DOMAIN, EC1 JRNL REF VIRUSES V. 13 159 2021 JRNL REFN ESSN 1999-4915 JRNL DOI 10.3390/V13020159 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PONDEROSA-C/S, X-PLOR NIH REMARK 3 AUTHORS : LEE, PETIT, CORNILESCU, STARK AND MARKLEY REMARK 3 (PONDEROSA-C/S), SCHWIETERS, KUSZEWSKI, TJANDRA REMARK 3 AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7KNV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1000251771. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 380 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.4 MM [U-100% 13C; U-100% 15N] REMARK 210 CDHR3 EXTRACELLULAR DOMAIN EC1, REMARK 210 50 MM HEPES, 300 MM POTASSIUM REMARK 210 CHLORIDE, 10 MM CALCIUM CHLORIDE, REMARK 210 0.05 % W/V SODIUM AZIDE, 10 % V/ REMARK 210 V [U-100% 2H] D2O, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HN(CO)CA; 3D REMARK 210 HN(CA)CO; 3D HNCO; 3D HBHA(CO)NH; REMARK 210 3D HCCH-TOCSY; 3D HCCH-COSY; 3D REMARK 210 NOESY 1H-15N HSQC; 3D NOESY 1H- REMARK 210 13C HSQC ALIPHATIC; 2D 1H-13C REMARK 210 HSQC ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III; VNMR REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE, NMRFAM-SPARKY, REMARK 210 I-PINE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 ALA A 10 -45.99 -134.21 REMARK 500 1 LEU A 24 92.43 83.81 REMARK 500 1 GLU A 33 -161.96 51.03 REMARK 500 1 GLN A 61 148.65 -178.31 REMARK 500 1 ALA A 71 52.61 174.47 REMARK 500 1 SER A 78 146.16 -178.26 REMARK 500 1 THR A 87 88.02 66.21 REMARK 500 2 ASP A 15 -55.52 -133.79 REMARK 500 2 LEU A 24 92.47 84.98 REMARK 500 2 GLU A 33 -143.61 -62.03 REMARK 500 2 GLN A 61 145.03 -173.49 REMARK 500 2 SER A 78 147.12 -171.38 REMARK 500 3 LYS A 14 22.79 -151.72 REMARK 500 3 LEU A 24 92.51 87.10 REMARK 500 3 GLU A 33 -166.39 48.76 REMARK 500 3 ASN A 99 -51.04 -147.00 REMARK 500 4 LEU A 24 92.99 86.48 REMARK 500 4 ALA A 27 127.19 -170.93 REMARK 500 4 GLU A 33 -170.14 52.93 REMARK 500 4 GLN A 61 150.00 -173.90 REMARK 500 4 ALA A 71 86.67 61.44 REMARK 500 4 SER A 78 147.24 -170.06 REMARK 500 5 LEU A 24 92.62 88.22 REMARK 500 5 ALA A 27 120.33 -170.17 REMARK 500 5 GLU A 33 -138.95 -60.44 REMARK 500 5 GLN A 61 147.42 -173.54 REMARK 500 5 THR A 87 86.27 76.23 REMARK 500 5 THR A 133 95.54 52.75 REMARK 500 6 LEU A 24 92.27 78.60 REMARK 500 6 ALA A 27 128.79 -170.66 REMARK 500 6 GLU A 33 -164.06 63.61 REMARK 500 6 SER A 78 146.43 -172.44 REMARK 500 6 THR A 86 72.81 -69.42 REMARK 500 7 ALA A 10 -35.68 -169.65 REMARK 500 7 LYS A 14 -87.60 51.35 REMARK 500 7 ASP A 15 16.31 48.75 REMARK 500 7 LEU A 24 92.12 85.53 REMARK 500 7 ALA A 32 70.12 -105.42 REMARK 500 7 GLU A 33 -157.62 57.11 REMARK 500 7 GLN A 61 144.49 -175.00 REMARK 500 7 SER A 78 147.02 -170.05 REMARK 500 7 THR A 87 102.30 62.53 REMARK 500 8 LYS A 14 26.24 -168.68 REMARK 500 8 LEU A 24 92.90 84.89 REMARK 500 8 GLU A 33 -145.97 34.62 REMARK 500 8 GLN A 61 149.15 -174.61 REMARK 500 8 ALA A 71 70.18 65.33 REMARK 500 8 LEU A 77 -62.76 -91.98 REMARK 500 8 THR A 87 98.42 100.02 REMARK 500 9 LEU A 24 92.20 84.02 REMARK 500 REMARK 500 THIS ENTRY HAS 122 RAMACHANDRAN OUTLIERS. 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 CA A 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 33 OE2 REMARK 620 2 GLU A 95 OE2 120.0 REMARK 620 3 ASP A 125 OD1 84.5 123.8 REMARK 620 4 ASP A 125 OD2 128.0 105.1 47.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 95 OE1 REMARK 620 2 GLU A 95 OE2 42.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 203 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 126 O REMARK 620 2 ASN A 127 OD1 98.3 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30812 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF CDHR3 EXTRACELLULAR DOMAIN EC1 DBREF 7KNV A 21 130 UNP Q6ZTQ4 CDHR3_HUMAN 21 130 SEQADV 7KNV MET A 9 UNP Q6ZTQ4 INITIATING METHIONINE SEQADV 7KNV ALA A 10 UNP Q6ZTQ4 EXPRESSION TAG SEQADV 7KNV SER A 11 UNP Q6ZTQ4 EXPRESSION TAG SEQADV 7KNV ASP A 12 UNP Q6ZTQ4 EXPRESSION TAG SEQADV 7KNV TYR A 13 UNP Q6ZTQ4 EXPRESSION TAG SEQADV 7KNV LYS A 14 UNP Q6ZTQ4 EXPRESSION TAG SEQADV 7KNV ASP A 15 UNP Q6ZTQ4 EXPRESSION TAG SEQADV 7KNV ASP A 16 UNP Q6ZTQ4 EXPRESSION TAG SEQADV 7KNV ASP A 17 UNP Q6ZTQ4 EXPRESSION TAG SEQADV 7KNV ASP A 18 UNP Q6ZTQ4 EXPRESSION TAG SEQADV 7KNV LYS A 19 UNP Q6ZTQ4 EXPRESSION TAG SEQADV 7KNV LEU A 20 UNP Q6ZTQ4 EXPRESSION TAG SEQADV 7KNV GLY A 131 UNP Q6ZTQ4 EXPRESSION TAG SEQADV 7KNV GLY A 132 UNP Q6ZTQ4 EXPRESSION TAG SEQADV 7KNV THR A 133 UNP Q6ZTQ4 EXPRESSION TAG SEQADV 7KNV LYS A 134 UNP Q6ZTQ4 EXPRESSION TAG SEQRES 1 A 126 MET ALA SER ASP TYR LYS ASP ASP ASP ASP LYS LEU HIS SEQRES 2 A 126 LEU ILE LEU LEU PRO ALA THR GLY ASN VAL ALA GLU ASN SEQRES 3 A 126 SER PRO PRO GLY THR SER VAL HIS LYS PHE SER VAL LYS SEQRES 4 A 126 LEU SER ALA SER LEU SER PRO VAL ILE PRO GLY PHE PRO SEQRES 5 A 126 GLN ILE VAL ASN SER ASN PRO LEU THR GLU ALA PHE ARG SEQRES 6 A 126 VAL ASN TRP LEU SER GLY THR TYR PHE GLU VAL VAL THR SEQRES 7 A 126 THR GLY MET GLU GLN LEU ASP PHE GLU THR GLY PRO ASN SEQRES 8 A 126 ILE PHE ASP LEU GLN ILE TYR VAL LYS ASP GLU VAL GLY SEQRES 9 A 126 VAL THR ASP LEU GLN VAL LEU THR VAL GLN VAL THR ASP SEQRES 10 A 126 VAL ASN GLU PRO PRO GLY GLY THR LYS HET CA A 201 1 HET CA A 202 1 HET CA A 203 1 HETNAM CA CALCIUM ION FORMUL 2 CA 3(CA 2+) HELIX 1 AA1 ASP A 93 GLY A 97 5 5 SHEET 1 AA1 4 LEU A 22 ILE A 23 0 SHEET 2 AA1 4 SER A 40 VAL A 46 -1 O SER A 45 N ILE A 23 SHEET 3 AA1 4 TYR A 81 THR A 86 -1 O PHE A 82 N PHE A 44 SHEET 4 AA1 4 PHE A 72 SER A 78 -1 N SER A 78 O TYR A 81 SHEET 1 AA2 4 THR A 28 VAL A 31 0 SHEET 2 AA2 4 THR A 114 VAL A 123 1 O GLN A 122 N GLY A 29 SHEET 3 AA2 4 ILE A 100 LYS A 108 -1 N ILE A 105 O GLN A 117 SHEET 4 AA2 4 ILE A 62 ASN A 64 -1 N VAL A 63 O GLN A 104 LINK OE2 GLU A 33 CA CA A 201 1555 1555 2.29 LINK OE2 GLU A 95 CA CA A 201 1555 1555 2.59 LINK OE1 GLU A 95 CA CA A 202 1555 1555 3.14 LINK OE2 GLU A 95 CA CA A 202 1555 1555 2.81 LINK OD1 ASP A 125 CA CA A 201 1555 1555 2.28 LINK OD2 ASP A 125 CA CA A 201 1555 1555 2.90 LINK O VAL A 126 CA CA A 203 1555 1555 3.14 LINK OD1 ASN A 127 CA CA A 203 1555 1555 2.89 CISPEP 1 PRO A 26 ALA A 27 1 -1.87 CISPEP 2 PRO A 60 GLN A 61 1 -0.97 CISPEP 3 PRO A 67 LEU A 68 1 -0.60 CISPEP 4 PRO A 26 ALA A 27 2 -0.67 CISPEP 5 PRO A 60 GLN A 61 2 -2.18 CISPEP 6 PRO A 67 LEU A 68 2 -0.87 CISPEP 7 PRO A 26 ALA A 27 3 -1.48 CISPEP 8 PRO A 60 GLN A 61 3 -1.66 CISPEP 9 PRO A 67 LEU A 68 3 -0.97 CISPEP 10 PRO A 26 ALA A 27 4 -2.43 CISPEP 11 PRO A 60 GLN A 61 4 -0.96 CISPEP 12 PRO A 67 LEU A 68 4 -0.17 CISPEP 13 PRO A 26 ALA A 27 5 -1.78 CISPEP 14 PRO A 60 GLN A 61 5 -1.07 CISPEP 15 PRO A 67 LEU A 68 5 -0.16 CISPEP 16 PRO A 26 ALA A 27 6 -2.21 CISPEP 17 PRO A 60 GLN A 61 6 -0.44 CISPEP 18 PRO A 67 LEU A 68 6 -1.27 CISPEP 19 PRO A 26 ALA A 27 7 -1.91 CISPEP 20 PRO A 60 GLN A 61 7 -1.01 CISPEP 21 PRO A 67 LEU A 68 7 -0.28 CISPEP 22 PRO A 26 ALA A 27 8 -1.84 CISPEP 23 PRO A 60 GLN A 61 8 -1.11 CISPEP 24 PRO A 67 LEU A 68 8 0.19 CISPEP 25 PRO A 26 ALA A 27 9 -1.61 CISPEP 26 PRO A 60 GLN A 61 9 -1.74 CISPEP 27 PRO A 67 LEU A 68 9 0.09 CISPEP 28 PRO A 26 ALA A 27 10 -2.22 CISPEP 29 PRO A 60 GLN A 61 10 0.44 CISPEP 30 PRO A 67 LEU A 68 10 -0.54 CISPEP 31 PRO A 26 ALA A 27 11 -2.44 CISPEP 32 PRO A 60 GLN A 61 11 -0.08 CISPEP 33 PRO A 67 LEU A 68 11 -0.37 CISPEP 34 PRO A 26 ALA A 27 12 -2.88 CISPEP 35 PRO A 60 GLN A 61 12 -1.28 CISPEP 36 PRO A 67 LEU A 68 12 -0.98 CISPEP 37 PRO A 26 ALA A 27 13 -1.66 CISPEP 38 PRO A 60 GLN A 61 13 -1.66 CISPEP 39 PRO A 67 LEU A 68 13 -1.12 CISPEP 40 PRO A 26 ALA A 27 14 -1.85 CISPEP 41 PRO A 60 GLN A 61 14 -0.23 CISPEP 42 PRO A 67 LEU A 68 14 -1.07 CISPEP 43 PRO A 26 ALA A 27 15 -1.66 CISPEP 44 PRO A 60 GLN A 61 15 -1.29 CISPEP 45 PRO A 67 LEU A 68 15 0.04 CISPEP 46 PRO A 26 ALA A 27 16 -2.09 CISPEP 47 PRO A 60 GLN A 61 16 -1.23 CISPEP 48 PRO A 67 LEU A 68 16 -0.73 CISPEP 49 PRO A 26 ALA A 27 17 -2.13 CISPEP 50 PRO A 60 GLN A 61 17 -1.39 CISPEP 51 PRO A 67 LEU A 68 17 0.18 CISPEP 52 PRO A 26 ALA A 27 18 -2.79 CISPEP 53 PRO A 60 GLN A 61 18 -1.13 CISPEP 54 PRO A 67 LEU A 68 18 -0.03 CISPEP 55 PRO A 26 ALA A 27 19 -1.50 CISPEP 56 PRO A 60 GLN A 61 19 -0.12 CISPEP 57 PRO A 67 LEU A 68 19 -0.22 CISPEP 58 PRO A 26 ALA A 27 20 -2.55 CISPEP 59 PRO A 60 GLN A 61 20 -1.03 CISPEP 60 PRO A 67 LEU A 68 20 -0.13 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 MODEL 1