HEADER IMMUNE SYSTEM 21-MAY-13 3J3Z TITLE STRUCTURE OF MA28-7 NEUTRALIZING ANTIBODY FAB FRAGMENT FROM ELECTRON TITLE 2 CRYO-MICROSCOPY OF ENTEROVIRUS 71 COMPLEXED WITH A FAB FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: MA28-7 NEUTRALIZING ANTIBODY LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 FRAGMENT: FAB; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: MA28-7 NEUTRALIZING ANTIBODY HEAVY CHAIN; COMPND 7 CHAIN: H; COMPND 8 FRAGMENT: FAB SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 7 ORGANISM_COMMON: MOUSE; SOURCE 8 ORGANISM_TAXID: 10090 KEYWDS EV71, ENTEROVIRUS, HFMD, STRAIN-SPECIFIC EPTITOPE, VP1-145, IMMUNE KEYWDS 2 SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR H.LEE,J.O.CIFUENTE,R.E.ASHLEY,J.F.CONWAY,A.M.MAKHOV,Y.TANO,H.SHIMIZU, AUTHOR 2 Y.NISHIMURA,S.HAFENSTEIN REVDAT 4 18-JUL-18 3J3Z 1 REMARK REVDAT 3 09-APR-14 3J3Z 1 SOURCE REVDAT 2 06-NOV-13 3J3Z 1 JRNL REVDAT 1 28-AUG-13 3J3Z 0 JRNL AUTH H.LEE,J.O.CIFUENTE,R.E.ASHLEY,J.F.CONWAY,A.M.MAKHOV,Y.TANO, JRNL AUTH 2 H.SHIMIZU,Y.NISHIMURA,S.HAFENSTEIN JRNL TITL A STRAIN-SPECIFIC EPITOPE OF ENTEROVIRUS 71 IDENTIFIED BY JRNL TITL 2 CRYO-ELECTRON MICROSCOPY OF THE COMPLEX WITH FAB FROM JRNL TITL 3 NEUTRALIZING ANTIBODY. JRNL REF J.VIROL. V. 87 11363 2013 JRNL REFN ISSN 0022-538X JRNL PMID 23946455 JRNL DOI 10.1128/JVI.01926-13 REMARK 2 REMARK 2 RESOLUTION. 23.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : UCSF CHIMERA, EMAN REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 3GK8 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : CORRELATION COEFFICIENT REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : REFINEMENT PROTOCOL--RIGID BODY DETAILS--THE REMARK 3 FAB STRUCTURE WAS FITTED MANUALLY, THEN REFINED IN CHIMERA. REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : 1.230 REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 23.40 REMARK 3 NUMBER OF PARTICLES : 27026 REMARK 3 CTF CORRECTION METHOD : NULL REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: THE BREAKSYM OPTION IN EMAN2 WAS USED TO SEARCH FOR REMARK 3 THE ICOSAHEDRALLY-RELATED ORIENTATIONS. (SINGLE PARTICLE DETAILS: REMARK 3 SELECTED PARTICLES WERE LOW-PASS FILTERED AT 10 ANGSTROM. REMARK 3 ASYMMETRIC RECONSTRUCTION WAS PERFORMED WITH THE BREAKSYM OPTION REMARK 3 IN EMAN2.) (SINGLE PARTICLE--APPLIED SYMMETRY: C1) REMARK 4 REMARK 4 3J3Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000160221. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : ENTEROVIRUS 71 COMPLEXED WITH REMARK 245 FAB FRAGMENT OF MA28-7 REMARK 245 NEUTRALIZING ANTIBODY REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : GLOW-DISCHARGED HOLEY CARBON REMARK 245 QUANTIFOIL ELECTRON MICROSCOPY REMARK 245 GRIDS REMARK 245 SAMPLE VITRIFICATION DETAILS : PLUNGED INTO ETHANE-PROPANE REMARK 245 MIXTURE (FEI VITROBOT MARK III) REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 02-FEB-11 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : 95.00 REMARK 245 MICROSCOPE MODEL : FEI TECNAI F20 REMARK 245 DETECTOR TYPE : KODAK SO-163 FILM REMARK 245 MINIMUM DEFOCUS (NM) : 1900.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 6120.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 NOMINAL CS : 2.00 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 15.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : 50000 REMARK 245 CALIBRATED MAGNIFICATION : 48425 REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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 APPLY THE FOLLOWING TO CHAINS: L, H 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLY H 56 N - CA - C ANGL. DEV. = -16.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ASN L 30 -112.88 52.27 REMARK 500 ALA L 51 -45.91 70.06 REMARK 500 SER L 52 33.20 -146.81 REMARK 500 SER L 67 109.66 -176.68 REMARK 500 LYS H 11 75.32 -117.32 REMARK 500 ALA H 14 75.41 -62.86 REMARK 500 SER H 15 -54.17 -179.65 REMARK 500 ASP H 55 88.49 87.06 REMARK 500 SER H 57 -112.85 49.31 REMARK 500 ARG H 59 105.80 -178.01 REMARK 500 LYS H 65 -98.14 -22.67 REMARK 500 ASP H 73 114.36 -167.81 REMARK 500 LYS H 74 -164.76 -71.45 REMARK 500 SER H 75 11.78 58.38 REMARK 500 SER H 76 -8.67 -162.75 REMARK 500 ASN H 83 102.35 61.76 REMARK 500 ARG H 84 -90.72 -86.53 REMARK 500 THR H 86 121.81 66.68 REMARK 500 SER H 87 -39.01 175.83 REMARK 500 ALA H 91 -169.03 177.03 REMARK 500 TYR H 104 5.26 -68.64 REMARK 500 ALA H 136 -133.21 47.01 REMARK 500 ALA H 137 42.65 -179.70 REMARK 500 LEU H 177 -166.12 -57.39 REMARK 500 ALA H 178 38.61 127.92 REMARK 500 ASP H 179 -41.97 83.29 REMARK 500 TYR H 181 130.57 -17.22 REMARK 500 SER H 198 151.13 -42.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-5673 RELATED DB: EMDB DBREF 3J3Z L 1 214 PDB 3J3Z 3J3Z 1 214 DBREF 3J3Z H 1 220 PDB 3J3Z 3J3Z 1 220 SEQRES 1 L 214 ASP ILE VAL MET THR GLN SER HIS LYS PHE MET SER THR SEQRES 2 L 214 SER VAL GLY ASP ARG VAL SER ILE THR CYS LYS ALA SER SEQRES 3 L 214 GLN ASP VAL ASN THR ALA LEU ALA TRP TYR GLN GLN ILE SEQRES 4 L 214 PRO GLY GLN SER PRO LYS LEU LEU ILE TYR SER ALA SER SEQRES 5 L 214 ASN ARG TYR THR GLY VAL PRO ASP ARG PHE THR ALA SER SEQRES 6 L 214 GLY SER GLY THR ASP PHE THR PHE THR ILE SER SER VAL SEQRES 7 L 214 GLN ALA GLU ASP LEU ALA LEU TYR TYR CYS GLN GLN HIS SEQRES 8 L 214 TYR THR THR PRO TRP THR PHE GLY GLY GLY THR LYS LEU SEQRES 9 L 214 GLU ILE LYS ARG ALA ASP ALA ALA PRO THR VAL SER ILE SEQRES 10 L 214 PHE PRO PRO SER SER GLU GLN LEU THR SER GLY GLY ALA SEQRES 11 L 214 SER VAL VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS ASP SEQRES 12 L 214 ILE ASN VAL LYS TRP ALA ILE ASP GLY ALA GLU ARG ALA SEQRES 13 L 214 GLY GLY VAL LEU ASN SER PHE THR GLY GLN ASP SER LYS SEQRES 14 L 214 ASP SER THR TYR SER MET SER SER THR LEU THR LEU THR SEQRES 15 L 214 LYS ASP GLU TYR GLU ARG HIS ALA SER TYR THR CYS GLU SEQRES 16 L 214 ALA THR HIS LYS THR SER THR ALA PRO ILE VAL LYS SER SEQRES 17 L 214 PHE ASN ARG GLY ALA ALA SEQRES 1 H 220 ALA VAL HIS LEU GLN GLY THR GLU LEU VAL LYS PRO GLY SEQRES 2 H 220 ALA SER ALA GLY VAL LYS LEU SER CYS LYS ALA SER GLY SEQRES 3 H 220 TYR THR PHE THR ASN TYR ASP MET ASN TRP VAL ARG GLN SEQRES 4 H 220 ARG PRO GLU GLN GLY LEU GLU TRP ILE GLY TRP ILE PHE SEQRES 5 H 220 PRO GLY ASP GLY SER THR ARG TYR ASN GLU LYS PHE LYS SEQRES 6 H 220 GLY LYS ALA THR LEU THR THR ASP LYS SER SER SER THR SEQRES 7 H 220 ALA TYR GLN LEU ASN ARG LEU THR SER GLU ASP SER ALA SEQRES 8 H 220 VAL TYR PHE CYS ALA ARG ARG GLY PHE HIS GLY SER TYR SEQRES 9 H 220 SER PHE ALA TYR TRP GLY GLN GLY THR LEU VAL THR VAL SEQRES 10 H 220 SER GLY ALA LYS THR THR ALA PRO SER VAL TYR PRO LEU SEQRES 11 H 220 ALA PRO ALA ALA GLY ALA ALA GLY ALA GLY SER SER VAL SEQRES 12 H 220 THR LEU GLY CYS LEU VAL LYS GLY TYR PHE PRO GLU PRO SEQRES 13 H 220 VAL THR LEU THR TRP ASN SER GLY SER LEU SER SER GLY SEQRES 14 H 220 VAL HIS THR PHE PRO ALA VAL LEU ALA ASP LEU TYR THR SEQRES 15 H 220 LEU SER SER SER VAL THR VAL THR SER SER THR TRP PRO SEQRES 16 H 220 ALA GLU SER ILE THR CYS ASN VAL ALA HIS PRO ALA SER SEQRES 17 H 220 SER THR LYS VAL ASP LYS LYS ILE GLU PRO ARG GLY HELIX 1 1 GLN L 79 LEU L 83 5 5 HELIX 2 2 SER L 121 SER L 127 1 7 HELIX 3 3 LYS L 183 GLU L 187 1 5 HELIX 4 4 THR H 28 TYR H 32 5 5 HELIX 5 5 GLU H 62 LYS H 65 5 4 HELIX 6 6 SER H 163 SER H 165 5 3 HELIX 7 7 SER H 192 TRP H 194 5 3 HELIX 8 8 PRO H 206 SER H 209 5 4 SHEET 1 A 4 MET L 4 THR L 5 0 SHEET 2 A 4 VAL L 19 ALA L 25 -1 O LYS L 24 N THR L 5 SHEET 3 A 4 ASP L 70 ILE L 75 -1 O PHE L 71 N CYS L 23 SHEET 4 A 4 PHE L 62 GLY L 66 -1 N THR L 63 O THR L 74 SHEET 1 B 6 PHE L 10 THR L 13 0 SHEET 2 B 6 THR L 102 ILE L 106 1 O GLU L 105 N THR L 13 SHEET 3 B 6 LEU L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 B 6 LEU L 33 GLN L 38 -1 N ALA L 34 O GLN L 89 SHEET 5 B 6 LYS L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 B 6 ASN L 53 ARG L 54 -1 O ASN L 53 N TYR L 49 SHEET 1 C 4 PHE L 10 THR L 13 0 SHEET 2 C 4 THR L 102 ILE L 106 1 O GLU L 105 N THR L 13 SHEET 3 C 4 LEU L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 C 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 D 4 THR L 114 PHE L 118 0 SHEET 2 D 4 GLY L 129 PHE L 139 -1 O VAL L 133 N PHE L 118 SHEET 3 D 4 TYR L 173 THR L 182 -1 O LEU L 179 N VAL L 132 SHEET 4 D 4 VAL L 159 THR L 164 -1 N SER L 162 O SER L 176 SHEET 1 E 4 ALA L 153 ARG L 155 0 SHEET 2 E 4 ASN L 145 ILE L 150 -1 N ILE L 150 O ALA L 153 SHEET 3 E 4 SER L 191 THR L 197 -1 O GLU L 195 N LYS L 147 SHEET 4 E 4 ILE L 205 ASN L 210 -1 O ILE L 205 N ALA L 196 SHEET 1 F 4 HIS H 3 GLY H 6 0 SHEET 2 F 4 LEU H 20 SER H 25 -1 O LYS H 23 N GLN H 5 SHEET 3 F 4 THR H 78 GLN H 81 -1 O GLN H 81 N LEU H 20 SHEET 4 F 4 THR H 71 ASP H 73 -1 N THR H 71 O TYR H 80 SHEET 1 G 5 THR H 58 TYR H 60 0 SHEET 2 G 5 GLY H 44 ILE H 51 -1 N TRP H 50 O ARG H 59 SHEET 3 G 5 MET H 34 ARG H 40 -1 N ARG H 38 O GLU H 46 SHEET 4 G 5 ALA H 91 ARG H 97 -1 O PHE H 94 N VAL H 37 SHEET 5 G 5 TYR H 108 TRP H 109 -1 O TYR H 108 N ARG H 97 SHEET 1 H 5 THR H 58 TYR H 60 0 SHEET 2 H 5 GLY H 44 ILE H 51 -1 N TRP H 50 O ARG H 59 SHEET 3 H 5 MET H 34 ARG H 40 -1 N ARG H 38 O GLU H 46 SHEET 4 H 5 ALA H 91 ARG H 97 -1 O PHE H 94 N VAL H 37 SHEET 5 H 5 THR H 113 VAL H 115 -1 O THR H 113 N TYR H 93 SHEET 1 I 4 SER H 126 LEU H 130 0 SHEET 2 I 4 SER H 142 TYR H 152 -1 O LEU H 148 N TYR H 128 SHEET 3 I 4 TYR H 181 THR H 190 -1 O LEU H 183 N VAL H 149 SHEET 4 I 4 VAL H 170 THR H 172 -1 N HIS H 171 O SER H 186 SHEET 1 J 3 THR H 158 TRP H 161 0 SHEET 2 J 3 THR H 200 HIS H 205 -1 O ASN H 202 N THR H 160 SHEET 3 J 3 THR H 210 LYS H 215 -1 O THR H 210 N HIS H 205 SSBOND 1 CYS L 23 CYS L 88 1555 1555 2.03 SSBOND 2 CYS L 134 CYS L 194 1555 1555 2.03 SSBOND 3 CYS H 22 CYS H 95 1555 1555 2.03 SSBOND 4 CYS H 147 CYS H 201 1555 1555 2.05 CISPEP 1 THR L 94 PRO L 95 0 -0.07 CISPEP 2 TYR L 140 PRO L 141 0 1.72 CISPEP 3 PHE H 153 PRO H 154 0 -0.47 CISPEP 4 GLU H 155 PRO H 156 0 -0.26 CISPEP 5 TRP H 194 PRO H 195 0 0.45 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