HEADER IMMUNE SYSTEM 14-NOV-22 8HGJ TITLE TOXASCARIS LEONINA GALECTIN (TL-GAL) AND HUMAN T-CELL IMMUNOGLOBULIN TITLE 2 MUCIN-3 (TIM3) COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: GALECTIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEPATITIS A VIRUS CELLULAR RECEPTOR 2; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: HAVCR-2,T-CELL IMMUNOGLOBULIN AND MUCIN DOMAIN-CONTAINING COMPND 9 PROTEIN 3,TIMD-3,T-CELL IMMUNOGLOBULIN MUCIN RECEPTOR 3,TIM-3,T-CELL COMPND 10 MEMBRANE PROTEIN 3; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TOXASCARIS LEONINA; SOURCE 3 ORGANISM_COMMON: PARASITIC ROUNDWORM; SOURCE 4 ORGANISM_TAXID: 59264; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: HAVCR2, TIM3, TIMD3; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TL-GAL, T-CELL IMMUNOGLOBULIN MUCIN-3, TIM3, COMPLEX, IMMUNE SYSTEM EXPDTA ELECTRON MICROSCOPY AUTHOR C.W.HAN,S.B.JANG REVDAT 1 22-NOV-23 8HGJ 0 JRNL AUTH C.W.HAN,S.B.JANG JRNL TITL TOXASCARIS LEONINA GALECTIN (TL-GAL) AND HUMAN T-CELL JRNL TITL 2 IMMUNOGLOBULIN MUCIN-3 (TIM3) COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 4.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.820 REMARK 3 NUMBER OF PARTICLES : 946426 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8HGJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1300033582. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : TOXASCARIS LEONINA GALECTIN (TL REMARK 245 -GAL) AND HUMAN T-CELL REMARK 245 IMMUNOGLOBULIN MUCIN-3 (TIM3) REMARK 245 COMPLEX; GALECTIN; HEPATITIS A REMARK 245 VIRUS CELLULAR RECEPTOR 2 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL 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 : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS GLACIOS REMARK 245 DETECTOR TYPE : FEI FALCON III (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : -3000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : -1800.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : DARK FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 3999.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL 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: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS B 30 CA CYS B 30 CB 0.143 REMARK 500 CYS B 30 CB CYS B 30 SG 0.243 REMARK 500 CYS B 36 CB CYS B 36 SG 0.274 REMARK 500 CYS B 41 CB CYS B 41 SG 0.341 REMARK 500 CYS B 87 CB CYS B 87 SG 0.345 REMARK 500 REMARK 500 REMARK: NULL 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 CYS B 30 CA - CB - SG ANGL. DEV. = 21.5 DEGREES REMARK 500 CYS B 36 CA - CB - SG ANGL. DEV. = 13.0 DEGREES REMARK 500 CYS B 41 CA - CB - SG ANGL. DEV. = 26.0 DEGREES REMARK 500 CYS B 87 CA - CB - SG ANGL. DEV. = 31.5 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 GLU A 4 -61.93 -94.71 REMARK 500 THR A 5 23.68 44.08 REMARK 500 ALA A 47 -65.02 -109.71 REMARK 500 ASN A 52 -166.92 -77.35 REMARK 500 ASP A 63 -55.45 -128.09 REMARK 500 SER A 102 -1.79 -141.29 REMARK 500 GLN A 110 18.04 59.32 REMARK 500 ALA A 155 -70.13 -52.44 REMARK 500 ASP A 157 -26.66 -142.38 REMARK 500 LYS A 163 -168.60 -121.94 REMARK 500 GLU A 215 73.14 56.82 REMARK 500 GLU A 218 70.24 59.24 REMARK 500 ASN A 221 66.20 33.91 REMARK 500 PRO A 258 -164.08 -73.63 REMARK 500 HIS A 259 78.52 64.38 REMARK 500 ASP A 260 47.68 76.70 REMARK 500 ALA B 21 -70.63 -93.09 REMARK 500 PHE B 39 83.81 -154.33 REMARK 500 GLU B 40 106.00 -171.24 REMARK 500 ASP B 52 -167.74 -129.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 56 HIS A 57 146.44 REMARK 500 ASN A 85 PRO A 86 -149.95 REMARK 500 HIS A 179 ILE A 180 143.68 REMARK 500 PHE A 197 ASP A 198 149.61 REMARK 500 ARG A 255 LEU A 256 149.81 REMARK 500 PHE B 39 GLU B 40 138.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-34740 RELATED DB: EMDB REMARK 900 TOXASCARIS LEONINA GALECTIN (TL-GAL) AND HUMAN T-CELL REMARK 900 IMMUNOGLOBULIN MUCIN-3 (TIM3) COMPLEX DBREF1 8HGJ A 1 278 UNP A0A1L1QJZ7_TOXLN DBREF2 8HGJ A A0A1L1QJZ7 1 278 DBREF 8HGJ B 2 108 UNP Q8TDQ0 HAVR2_HUMAN 24 130 SEQRES 1 A 278 MET ALA THR GLU THR ASN TYR PRO VAL PRO TYR ARG SER SEQRES 2 A 278 LYS LEU THR GLU PRO PHE GLU PRO GLY GLN THR LEU ILE SEQRES 3 A 278 ILE LYS GLY LYS THR ALA GLU ASP SER VAL ARG PHE THR SEQRES 4 A 278 ILE ASN LEU HIS ASN THR SER ALA ASP PHE SER GLY ASN SEQRES 5 A 278 ASP VAL PRO LEU HIS ILE SER VAL ARG PHE ASP GLU GLY SEQRES 6 A 278 LYS ILE VAL PHE ASN THR PHE SER LYS GLY GLU TRP GLY SEQRES 7 A 278 LYS GLU GLU ARG LYS SER ASN PRO TYR LYS LYS GLY ASP SEQRES 8 A 278 ASP ILE ASP ILE ARG ILE ARG ALA HIS ASP SER LYS PHE SEQRES 9 A 278 SER ILE SER VAL ASP GLN LYS GLU VAL LYS GLU TYR GLU SEQRES 10 A 278 HIS ARG VAL PRO LEU SER SER VAL THR HIS PHE SER VAL SEQRES 11 A 278 ASP GLY ASP ILE LEU ILE THR TYR ILE HIS TRP GLY GLY SEQRES 12 A 278 LYS TYR TYR PRO VAL PRO TYR GLU SER GLY LEU ALA GLY SEQRES 13 A 278 ASP GLY LEU ALA PRO GLY LYS SER LEU LEU ILE PHE ALA SEQRES 14 A 278 THR PRO GLU LYS LYS GLY LYS ARG PHE HIS ILE ASN LEU SEQRES 15 A 278 LEU LYS LYS ASN GLY ASP ILE ALA LEU HIS PHE ASN PRO SEQRES 16 A 278 ARG PHE ASP GLU LYS ALA ILE VAL ARG ASN SER LEU ILE SEQRES 17 A 278 SER GLY GLU TRP GLY ASN GLU GLU ARG GLU GLY LYS ASN SEQRES 18 A 278 PRO LEU GLU LYS GLY ILE GLY CYS ASP LEU GLU PHE ARG SEQRES 19 A 278 ASN GLU GLU TYR ALA PHE GLN ILE TYR VAL ASP GLY GLU SEQRES 20 A 278 ARG PHE ALA THR TYR ALA HIS ARG LEU ASP PRO HIS ASP SEQRES 21 A 278 ILE ASN GLY LEU GLN ILE GLY GLY ASP VAL GLU VAL THR SEQRES 22 A 278 GLY ILE GLN MET VAL SEQRES 1 B 107 VAL GLU TYR ARG ALA GLU VAL GLY GLN ASN ALA TYR LEU SEQRES 2 B 107 PRO CYS PHE TYR THR PRO ALA ALA PRO GLY ASN LEU VAL SEQRES 3 B 107 PRO VAL CYS TRP GLY LYS GLY ALA CYS PRO VAL PHE GLU SEQRES 4 B 107 CYS GLY ASN VAL VAL LEU ARG THR ASP GLU ARG ASP VAL SEQRES 5 B 107 ASN TYR TRP THR SER ARG TYR TRP LEU ASN GLY ASP PHE SEQRES 6 B 107 ARG LYS GLY ASP VAL SER LEU THR ILE GLU ASN VAL THR SEQRES 7 B 107 LEU ALA ASP SER GLY ILE TYR CYS CYS ARG ILE GLN ILE SEQRES 8 B 107 PRO GLY ILE MET ASN ASP GLU LYS PHE ASN LEU LYS LEU SEQRES 9 B 107 VAL ILE LYS HELIX 1 AA1 ASP B 65 GLY B 69 5 5 SHEET 1 AA1 3 ASP A 92 ARG A 96 0 SHEET 2 AA1 3 GLN A 23 LYS A 30 -1 N GLY A 29 O ILE A 93 SHEET 3 AA1 3 TRP A 141 GLY A 143 -1 O GLY A 142 N THR A 24 SHEET 1 AA2 2 ILE A 40 LEU A 42 0 SHEET 2 AA2 2 LEU A 56 ILE A 58 -1 O ILE A 58 N ILE A 40 SHEET 1 AA3 2 PHE A 104 VAL A 108 0 SHEET 2 AA3 2 LYS A 111 TYR A 116 -1 O LYS A 114 N ILE A 106 SHEET 1 AA4 4 SER A 164 ILE A 167 0 SHEET 2 AA4 4 LEU A 231 ARG A 234 -1 O LEU A 231 N ILE A 167 SHEET 3 AA4 4 GLN A 241 VAL A 244 -1 O TYR A 243 N GLU A 232 SHEET 4 AA4 4 GLU A 247 THR A 251 -1 O ALA A 250 N ILE A 242 SHEET 1 AA5 2 ASN A 194 ARG A 196 0 SHEET 2 AA5 2 ALA A 201 VAL A 203 -1 O ALA A 201 N ARG A 196 SHEET 1 AA6 2 LEU A 207 ILE A 208 0 SHEET 2 AA6 2 GLU A 211 TRP A 212 -1 O GLU A 211 N ILE A 208 SHEET 1 AA7 2 GLY B 84 ILE B 90 0 SHEET 2 AA7 2 GLU B 99 LEU B 105 -1 O LEU B 103 N TYR B 86 SSBOND 1 CYS B 16 CYS B 88 1555 1555 2.02 SSBOND 2 CYS B 30 CYS B 41 1555 1555 2.16 SSBOND 3 CYS B 36 CYS B 87 1555 1555 2.17 CISPEP 1 VAL A 9 PRO A 10 0 -6.58 CISPEP 2 VAL A 148 PRO A 149 0 -12.73 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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