HEADER IMMUNE SYSTEM 18-APR-23 8J3V TITLE STRUCTURE OF THE TRANSMEMBRANE DOMAIN OF HUMAN PD-L2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PD-L2; COMPND 5 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: PDCD1LG2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PD-L2, TRANSMEMBRANE DOMAIN, TUMOR, LIGAND, IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR B.OUYANG,Y.ZHANG REVDAT 2 15-MAY-24 8J3V 1 REMARK REVDAT 1 13-MAR-24 8J3V 0 JRNL AUTH Y.ZHANG,T.XIAO,M.WEN,L.SHEN,L.DU,S.WEI,B.WU,Y.YU,S.WANG, JRNL AUTH 2 B.OUYANG JRNL TITL DECIPHERING CHOLESTEROL'S ROLE IN PD-L2 STABILITY: A JRNL TITL 2 DISTINCT REGULATORY MECHANISM FROM PD-L1. JRNL REF J.MOL.BIOL. V. 436 68500 2024 JRNL REFN ESSN 1089-8638 JRNL PMID 38401626 JRNL DOI 10.1016/J.JMB.2024.168500 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8J3V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1300036942. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 0.1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-15N] PD-L2_TM, 90% REMARK 210 H2O/10% D2O; 0.5 MM [U-13C; U- REMARK 210 15N] PD-L2_TM, 90% H2O/10% D2O; REMARK 210 0.5 MM [U-13C; U-15N; U-2H] PD- REMARK 210 L2_TM, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HN(CA)CO; REMARK 210 3D HN(CO)CA; 3D HNCACB; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH, XEASY, TOPSPIN, REMARK 210 NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SER A 253 -35.98 -136.29 REMARK 500 1 SER A 254 92.96 58.91 REMARK 500 1 ASP A 256 174.90 63.69 REMARK 500 1 THR A 263 115.44 62.75 REMARK 500 1 THR A 264 -47.42 -130.12 REMARK 500 1 GLU A 268 175.26 57.25 REMARK 500 2 HIS A 218 109.97 -54.30 REMARK 500 2 LEU A 251 -52.74 -165.32 REMARK 500 2 THR A 263 -36.49 -141.87 REMARK 500 2 THR A 264 90.51 48.04 REMARK 500 3 LYS A 250 95.24 53.25 REMARK 500 3 LEU A 251 -42.79 -141.91 REMARK 500 3 ASP A 256 162.50 61.15 REMARK 500 3 THR A 257 177.00 52.97 REMARK 500 3 ARG A 267 -66.61 71.34 REMARK 500 3 GLU A 268 99.12 58.87 REMARK 500 3 ASN A 270 178.12 59.17 REMARK 500 3 SER A 271 -76.23 65.70 REMARK 500 4 THR A 217 -58.41 74.17 REMARK 500 4 HIS A 218 77.50 -113.94 REMARK 500 4 ASP A 256 173.01 58.01 REMARK 500 4 THR A 265 51.48 -118.84 REMARK 500 4 LYS A 266 -45.58 -132.55 REMARK 500 4 ARG A 267 35.03 -152.33 REMARK 500 4 SER A 271 31.21 -141.68 REMARK 500 5 THR A 217 44.98 -166.90 REMARK 500 5 THR A 257 -40.47 -178.32 REMARK 500 5 THR A 263 98.16 58.07 REMARK 500 5 THR A 265 88.35 47.12 REMARK 500 5 ARG A 267 176.54 57.02 REMARK 500 5 GLU A 268 151.93 62.80 REMARK 500 5 ALA A 272 -49.03 -153.88 REMARK 500 6 LEU A 251 96.08 64.98 REMARK 500 6 TYR A 252 -59.79 -144.62 REMARK 500 6 THR A 265 92.86 52.85 REMARK 500 6 ASN A 270 90.93 56.61 REMARK 500 7 SER A 253 68.93 -156.26 REMARK 500 7 ASP A 256 50.62 -145.30 REMARK 500 7 THR A 257 56.77 -99.98 REMARK 500 7 THR A 258 99.43 59.17 REMARK 500 7 GLU A 268 -40.01 -173.00 REMARK 500 7 SER A 271 -72.58 69.21 REMARK 500 7 ALA A 272 -42.05 -175.49 REMARK 500 8 TYR A 252 -69.33 70.91 REMARK 500 8 LYS A 255 100.75 59.51 REMARK 500 8 ARG A 267 -179.04 55.52 REMARK 500 9 THR A 217 -72.09 -142.91 REMARK 500 9 LYS A 250 131.26 64.15 REMARK 500 9 TYR A 252 29.32 -175.42 REMARK 500 9 THR A 257 93.93 47.72 REMARK 500 REMARK 500 THIS ENTRY HAS 97 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36560 RELATED DB: BMRB REMARK 900 STRUCTURE OF THE TRANSMEMBRANE DOMAIN OF HUMAN PD-L2 DBREF 8J3V A 214 273 UNP Q9BQ51 PD1L2_HUMAN 214 273 SEQADV 8J3V SER A 230 UNP Q9BQ51 CYS 230 CONFLICT SEQADV 8J3V SER A 248 UNP Q9BQ51 CYS 248 CONFLICT SEQRES 1 A 60 GLU PRO ARG THR HIS PRO THR TRP LEU LEU HIS ILE PHE SEQRES 2 A 60 ILE PRO PHE SER ILE ILE ALA PHE ILE PHE ILE ALA THR SEQRES 3 A 60 VAL ILE ALA LEU ARG LYS GLN LEU SER GLN LYS LEU TYR SEQRES 4 A 60 SER SER LYS ASP THR THR LYS ARG PRO VAL THR THR THR SEQRES 5 A 60 LYS ARG GLU VAL ASN SER ALA ILE HELIX 1 AA1 PRO A 219 LEU A 251 1 33 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