HEADER MEMBRANE PROTEIN 13-DEC-24 9L16 TITLE A LOCAL CRYO_EM STRUCTURE OF CCR7 COMPLEX WITH CCL21 COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-C MOTIF CHEMOKINE 21; COMPND 3 CHAIN: L; COMPND 4 SYNONYM: 6CKINE,BETA-CHEMOKINE EXODUS-2,SECONDARY LYMPHOID-TISSUE COMPND 5 CHEMOKINE,SLC,SMALL-INDUCIBLE CYTOKINE A21; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: C-C CHEMOKINE RECEPTOR TYPE 7; COMPND 9 CHAIN: R; COMPND 10 SYNONYM: C-C CKR-7,CC-CKR-7,CCR-7,BLR2,CDW197,EPSTEIN-BARR VIRUS- COMPND 11 INDUCED G-PROTEIN COUPLED RECEPTOR 1,EBI1,EBV-INDUCED G-PROTEIN COMPND 12 COUPLED RECEPTOR 1,MIP-3 BETA RECEPTOR; COMPND 13 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: CCL21, SCYA21, UNQ784/PRO1600; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: CCR7, CMKBR7, EBI1, EVI1; SOURCE 13 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS GPCR, CCL21, CCR7, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR J.DUAN,Q.YUAN,Y.CAO REVDAT 1 17-DEC-25 9L16 0 JRNL AUTH J.DUAN,Q.YUAN,Y.CAO JRNL TITL A LOCAL CRYO_EM STRUCTURE OF CCR7 COMPLEX WITH CCL21 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, CRYOSPARC 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) : 3.500 REMARK 3 NUMBER OF PARTICLES : 469279 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 9L16 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 17-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1300054716. 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 : A LOCAL CRYO_EM STRUCTURE OF REMARK 245 CCR7 COMPLEX WITH CCR21 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 : 7.04 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 KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 8000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 18000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 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, R 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLN L 74 REMARK 465 LYS L 75 REMARK 465 PRO L 76 REMARK 465 ALA L 77 REMARK 465 GLN L 78 REMARK 465 GLN R 25 REMARK 465 ASP R 26 REMARK 465 GLU R 27 REMARK 465 VAL R 28 REMARK 465 THR R 29 REMARK 465 CYS R 346 REMARK 465 LEU R 347 REMARK 465 SER R 348 REMARK 465 GLN R 349 REMARK 465 GLU R 350 REMARK 465 GLN R 351 REMARK 465 LEU R 352 REMARK 465 ARG R 353 REMARK 465 GLN R 354 REMARK 465 TRP R 355 REMARK 465 SER R 356 REMARK 465 SER R 357 REMARK 465 CYS R 358 REMARK 465 ARG R 359 REMARK 465 HIS R 360 REMARK 465 ILE R 361 REMARK 465 ARG R 362 REMARK 465 ARG R 363 REMARK 465 SER R 364 REMARK 465 SER R 365 REMARK 465 MET R 366 REMARK 465 SER R 367 REMARK 465 VAL R 368 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN L 6 CG CD OE1 NE2 REMARK 470 GLN L 14 CG CD OE1 NE2 REMARK 470 ARG L 15 CG CD NE CZ NH1 NH2 REMARK 470 LYS L 16 CG CD CE NZ REMARK 470 LYS L 20 CG CD CE NZ REMARK 470 LYS L 27 CG CD CE NZ REMARK 470 LYS L 45 CG CD CE NZ REMARK 470 ARG L 46 CG CD NE CZ NH1 NH2 REMARK 470 LYS L 56 CG CD CE NZ REMARK 470 LYS L 69 CG CD CE NZ REMARK 470 ASP R 30 CG OD1 OD2 REMARK 470 ASP R 31 CG OD1 OD2 REMARK 470 TYR R 32 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ILE R 33 CG1 CG2 CD1 REMARK 470 ASP R 35 CG OD1 OD2 REMARK 470 GLU R 45 CG CD OE1 OE2 REMARK 470 ARG R 54 CG CD NE CZ NH1 NH2 REMARK 470 MET R 64 CG SD CE REMARK 470 ASP R 104 CG OD1 OD2 REMARK 470 LYS R 120 CG CD CE NZ REMARK 470 SER R 121 OG REMARK 470 MET R 144 CG SD CE REMARK 470 GLN R 200 CG CD OE1 NE2 REMARK 470 ARG R 201 CG CD NE CZ NH1 NH2 REMARK 470 SER R 202 OG REMARK 470 GLU R 205 CG CD OE1 OE2 REMARK 470 GLN R 206 CG CD OE1 NE2 REMARK 470 GLU R 215 CG CD OE1 OE2 REMARK 470 GLU R 218 CG CD OE1 OE2 REMARK 470 ILE R 221 CG1 CG2 CD1 REMARK 470 ASP R 309 CG OD1 OD2 REMARK 470 ASN R 335 CG OD1 ND2 REMARK 470 LYS R 339 CG CD CE NZ REMARK 470 PHE R 341 CG CD1 CD2 CE1 CE2 CZ 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 ASP L 2 73.48 -62.73 REMARK 500 SER L 72 156.17 68.74 REMARK 500 ASP R 31 -60.85 -94.83 REMARK 500 GLN R 160 41.81 -108.80 REMARK 500 SER R 203 -106.73 43.36 REMARK 500 SER R 295 67.99 60.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62735 RELATED DB: EMDB REMARK 900 A LOCAL CRYO_EM STRUCTURE OF CCR7 COMPLEX WITH CCL21 DBREF 9L16 L 1 78 UNP O00585 CCL21_HUMAN 24 101 DBREF 9L16 R 25 368 UNP P32248 CCR7_HUMAN 25 368 SEQRES 1 L 78 SER ASP GLY GLY ALA GLN ASP CYS CYS LEU LYS TYR SER SEQRES 2 L 78 GLN ARG LYS ILE PRO ALA LYS VAL VAL ARG SER TYR ARG SEQRES 3 L 78 LYS GLN GLU PRO SER LEU GLY CYS SER ILE PRO ALA ILE SEQRES 4 L 78 LEU PHE LEU PRO ARG LYS ARG SER GLN ALA GLU LEU CYS SEQRES 5 L 78 ALA ASP PRO LYS GLU LEU TRP VAL GLN GLN LEU MET GLN SEQRES 6 L 78 HIS LEU ASP LYS THR PRO SER PRO GLN LYS PRO ALA GLN SEQRES 1 R 344 GLN ASP GLU VAL THR ASP ASP TYR ILE GLY ASP ASN THR SEQRES 2 R 344 THR VAL ASP TYR THR LEU PHE GLU SER LEU CYS SER LYS SEQRES 3 R 344 LYS ASP VAL ARG ASN PHE LYS ALA TRP PHE LEU PRO ILE SEQRES 4 R 344 MET TYR SER ILE ILE CYS PHE VAL GLY LEU LEU GLY ASN SEQRES 5 R 344 GLY LEU VAL VAL LEU THR TYR ILE TYR PHE LYS ARG LEU SEQRES 6 R 344 LYS THR MET THR ASP THR TYR LEU LEU ASN LEU ALA VAL SEQRES 7 R 344 ALA ASP ILE LEU PHE LEU LEU THR LEU PRO PHE TRP ALA SEQRES 8 R 344 TYR SER ALA ALA LYS SER TRP VAL PHE GLY VAL HIS PHE SEQRES 9 R 344 CYS LYS LEU ILE PHE ALA ILE TYR LYS MET SER PHE PHE SEQRES 10 R 344 SER GLY MET LEU LEU LEU LEU CYS ILE SER ILE ASP ARG SEQRES 11 R 344 TYR VAL ALA ILE VAL GLN ALA VAL SER ALA HIS ARG HIS SEQRES 12 R 344 ARG ALA ARG VAL LEU LEU ILE SER LYS LEU SER CYS VAL SEQRES 13 R 344 GLY ILE TRP ILE LEU ALA THR VAL LEU SER ILE PRO GLU SEQRES 14 R 344 LEU LEU TYR SER ASP LEU GLN ARG SER SER SER GLU GLN SEQRES 15 R 344 ALA MET ARG CYS SER LEU ILE THR GLU HIS VAL GLU ALA SEQRES 16 R 344 PHE ILE THR ILE GLN VAL ALA GLN MET VAL ILE GLY PHE SEQRES 17 R 344 LEU VAL PRO LEU LEU ALA MET SER PHE CYS TYR LEU VAL SEQRES 18 R 344 ILE ILE ARG THR LEU LEU GLN ALA ARG ASN PHE GLU ARG SEQRES 19 R 344 ASN LYS ALA ILE LYS VAL ILE ILE ALA VAL VAL VAL VAL SEQRES 20 R 344 PHE ILE VAL PHE GLN LEU PRO TYR ASN GLY VAL VAL LEU SEQRES 21 R 344 ALA GLN THR VAL ALA ASN PHE ASN ILE THR SER SER THR SEQRES 22 R 344 CYS GLU LEU SER LYS GLN LEU ASN ILE ALA TYR ASP VAL SEQRES 23 R 344 THR TYR SER LEU ALA CYS VAL ARG CYS CYS VAL ASN PRO SEQRES 24 R 344 PHE LEU TYR ALA PHE ILE GLY VAL LYS PHE ARG ASN ASP SEQRES 25 R 344 LEU PHE LYS LEU PHE LYS ASP LEU GLY CYS LEU SER GLN SEQRES 26 R 344 GLU GLN LEU ARG GLN TRP SER SER CYS ARG HIS ILE ARG SEQRES 27 R 344 ARG SER SER MET SER VAL HELIX 1 AA1 PRO L 18 LYS L 20 5 3 HELIX 2 AA2 GLU L 57 LEU L 67 1 11 HELIX 3 AA3 ASP R 40 PHE R 44 5 5 HELIX 4 AA4 LYS R 50 LYS R 87 1 38 HELIX 5 AA5 THR R 91 LYS R 120 1 30 HELIX 6 AA6 GLY R 125 VAL R 159 1 35 HELIX 7 AA7 GLN R 160 HIS R 165 1 6 HELIX 8 AA8 HIS R 167 SER R 190 1 24 HELIX 9 AA9 SER R 190 SER R 197 1 8 HELIX 10 AB1 HIS R 216 ILE R 230 1 15 HELIX 11 AB2 PHE R 232 LEU R 251 1 20 HELIX 12 AB3 ARG R 258 ASN R 292 1 35 HELIX 13 AB4 THR R 297 TYR R 326 1 30 HELIX 14 AB5 GLY R 330 ASP R 343 1 14 SHEET 1 AA1 3 VAL L 22 TYR L 25 0 SHEET 2 AA1 3 ILE L 39 PRO L 43 -1 O LEU L 42 N SER L 24 SHEET 3 AA1 3 LEU L 51 ALA L 53 -1 O ALA L 53 N ILE L 39 SHEET 1 AA2 2 ASP R 198 SER R 202 0 SHEET 2 AA2 2 GLN R 206 SER R 211 -1 O ARG R 209 N GLN R 200 SSBOND 1 CYS L 8 CYS L 34 1555 1555 2.03 SSBOND 2 CYS L 9 CYS L 52 1555 1555 2.03 SSBOND 3 CYS R 48 CYS R 298 1555 1555 2.03 SSBOND 4 CYS R 129 CYS R 210 1555 1555 2.03 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 TER 532 PRO L 73 TER 2970 GLY R 345 CONECT 46 235 CONECT 52 367 CONECT 235 46 CONECT 367 52 CONECT 661 2603 CONECT 1308 1926 CONECT 1926 1308 CONECT 2603 661 MASTER 201 0 0 14 5 0 0 6 2968 2 8 33 END