HEADER PROTEIN BINDING 02-JUN-20 7C8K TITLE STRUCTURAL BASIS FOR CROSS-SPECIES RECOGNITION OF COVID-19 VIRUS SPIKE TITLE 2 RECEPTOR BINDING DOMAIN TO BAT ACE2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANGIOTENSIN-CONVERTING ENZYME; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHINOLOPHUS MACROTIS; SOURCE 3 ORGANISM_COMMON: BIG-EARED HORSESHOE BAT; SOURCE 4 ORGANISM_TAXID: 196889; SOURCE 5 GENE: ACE2; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS COVID-19, RECEPTOR BINDING DOMAIN (RBD), RHINOLOPHUS MACROTIS, KEYWDS 2 PROTEIN BINDING EXPDTA ELECTRON MICROSCOPY AUTHOR K.F.LIU,J.WANG,S.G.TAN,S.NIU,L.L.WU,Y.F.ZHANG,X.Q.PAN,Y.M.MENG, AUTHOR 2 Q.CHEN,Q.H.WANG,H.W.WANG,J.X.QI,G.F.GAO REVDAT 2 23-OCT-24 7C8K 1 REMARK REVDAT 1 27-JAN-21 7C8K 0 JRNL AUTH K.LIU,S.TAN,S.NIU,J.WANG,L.WU,H.SUN,Y.ZHANG,X.PAN,X.QU,P.DU, JRNL AUTH 2 Y.MENG,Y.JIA,Q.CHEN,C.DENG,J.YAN,H.W.WANG,Q.WANG,J.QI, JRNL AUTH 3 G.F.GAO JRNL TITL CROSS-SPECIES RECOGNITION OF SARS-COV-2 TO BAT ACE2. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 33335073 JRNL DOI 10.1073/PNAS.2020216118 REMARK 2 REMARK 2 RESOLUTION. 3.20 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 62289 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 7C8K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1300017183. 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 : BAT ACE2 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 : 8.00 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 : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : NULL REMARK 245 MAXIMUM DEFOCUS (NM) : NULL 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: MONOMERIC 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 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 LYS A 134 CD CE NZ REMARK 470 ASN A 136 OD1 ND2 REMARK 470 GLU A 210 CG CD OE1 OE2 REMARK 470 GLU A 211 CG CD OE1 OE2 REMARK 470 ILE A 229 CG2 CD1 REMARK 470 THR A 231 CG2 REMARK 470 ASP A 250 CG OD1 OD2 REMARK 470 THR A 251 OG1 CG2 REMARK 470 SER A 319 OG REMARK 470 MET A 421 CG SD CE REMARK 470 ARG A 429 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 471 CG CD OE1 OE2 REMARK 470 GLU A 472 CG CD OE1 OE2 REMARK 470 GLN A 534 CG CD OE1 NE2 REMARK 470 ASN A 536 CG OD1 ND2 REMARK 470 ASP A 549 CG OD1 OD2 REMARK 470 LYS A 552 CG CD CE NZ REMARK 470 GLN A 556 CG CD OE1 NE2 REMARK 470 LYS A 568 CD CE NZ REMARK 470 ASP A 572 CG OD1 OD2 REMARK 470 ILE A 573 CG1 CG2 CD1 REMARK 470 ASP A 575 CG OD1 OD2 REMARK 470 SER A 576 OG REMARK 470 ARG A 577 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 580 CG OD1 OD2 REMARK 470 LYS A 589 CD CE NZ REMARK 470 GLU A 597 CD OE1 OE2 REMARK 470 ARG A 600 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 601 CG CD CE NZ REMARK 470 TYR A 603 CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN A 607 CG OD1 ND2 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 210 52.48 -91.31 REMARK 500 ASP A 338 -9.45 72.05 REMARK 500 TYR A 385 33.17 -98.39 REMARK 500 ALA A 507 50.21 -90.93 REMARK 500 ASN A 508 13.53 -142.93 REMARK 500 ARG A 577 30.86 -96.06 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 ZN A 705 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 374 NE2 REMARK 620 2 HIS A 378 NE2 94.9 REMARK 620 3 GLU A 402 OE2 100.5 100.5 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-30306 RELATED DB: EMDB REMARK 900 STRUCTURAL BASIS FOR CROSS-SPECIES RECOGNITION OF COVID-19 VIRUS REMARK 900 SPIKE RECEPTOR BINDING DOMAIN TO BAT ACE2 DBREF 7C8K A 19 614 UNP E2DHI3 E2DHI3_RHIMR 19 614 SEQRES 1 A 596 SER THR THR GLU ASP GLU ALA LYS LYS PHE LEU ASP LYS SEQRES 2 A 596 PHE ASN SER LYS ALA GLU ASP LEU SER TYR GLU SER SER SEQRES 3 A 596 LEU ALA SER TRP ASP TYR ASN THR ASN ILE SER ASP GLU SEQRES 4 A 596 ASN VAL GLN LYS MET ASP GLU ALA GLY ALA LYS TRP SER SEQRES 5 A 596 ALA PHE TYR GLU GLU GLN SER LYS LEU ALA LYS ASN TYR SEQRES 6 A 596 PRO LEU GLU GLU ILE GLN ASN ASP THR VAL LYS ARG GLN SEQRES 7 A 596 LEU GLN ILE LEU GLN GLN SER GLY SER PRO VAL LEU SER SEQRES 8 A 596 GLU ASP LYS SER LYS ARG LEU ASN SER ILE LEU ASN ALA SEQRES 9 A 596 MET SER THR ILE TYR SER THR GLY LYS VAL CYS LYS PRO SEQRES 10 A 596 ASN ASN PRO GLN GLU CYS LEU LEU LEU GLU PRO GLY LEU SEQRES 11 A 596 ASP ASN ILE MET GLY THR SER LYS ASP TYR ASN GLU ARG SEQRES 12 A 596 LEU TRP ALA TRP GLU GLY TRP ARG ALA GLU VAL GLY LYS SEQRES 13 A 596 GLN LEU ARG PRO LEU TYR GLU GLU TYR VAL VAL LEU LYS SEQRES 14 A 596 ASN GLU MET ALA ARG GLY TYR HIS TYR GLU ASP TYR GLY SEQRES 15 A 596 ASP TYR TRP ARG ARG ASP TYR GLU THR GLU GLU SER SER SEQRES 16 A 596 GLY PRO GLY TYR SER ARG ASP GLN LEU MET LYS ASP VAL SEQRES 17 A 596 ASP ARG ILE PHE THR GLU ILE LYS PRO LEU TYR GLU HIS SEQRES 18 A 596 LEU HIS ALA TYR VAL ARG ALA LYS LEU MET ASP THR TYR SEQRES 19 A 596 PRO LEU HIS ILE SER PRO THR GLY CYS LEU PRO ALA HIS SEQRES 20 A 596 LEU LEU GLY ASP MET TRP GLY ARG PHE TRP THR ASN LEU SEQRES 21 A 596 TYR PRO LEU THR VAL PRO PHE GLY GLN LYS PRO ASN ILE SEQRES 22 A 596 ASP VAL THR ASP ALA MET LEU ASN GLN GLY TRP ASP ALA SEQRES 23 A 596 ASN ARG ILE PHE LYS GLU ALA GLU LYS PHE PHE VAL SER SEQRES 24 A 596 VAL SER LEU PRO LYS MET THR GLU GLY PHE TRP ASN LYS SEQRES 25 A 596 SER MET LEU THR GLU PRO GLY ASP GLY ARG LYS VAL VAL SEQRES 26 A 596 CYS HIS PRO THR ALA TRP ASP LEU GLY LYS GLY ASP PHE SEQRES 27 A 596 ARG ILE LYS MET CYS THR LYS VAL THR MET GLU ASP PHE SEQRES 28 A 596 LEU THR ALA HIS HIS GLU MET GLY HIS ILE GLN TYR ASP SEQRES 29 A 596 MET ALA TYR ALA SER GLN PRO TYR LEU LEU ARG ASN GLY SEQRES 30 A 596 ALA ASN GLU GLY PHE HIS GLU ALA VAL GLY GLU VAL MET SEQRES 31 A 596 SER LEU SER VAL ALA THR PRO LYS HIS LEU LYS THR MET SEQRES 32 A 596 GLY LEU LEU SER PRO ASP PHE ARG GLU ASP ASP GLU THR SEQRES 33 A 596 GLU ILE ASN PHE LEU LEU LYS GLN ALA LEU ASN ILE VAL SEQRES 34 A 596 GLY THR LEU PRO PHE THR TYR MET LEU GLU LYS TRP ARG SEQRES 35 A 596 TRP MET VAL PHE LYS GLY GLU ILE PRO LYS GLU GLU TRP SEQRES 36 A 596 MET LYS LYS TRP TRP GLU MET LYS ARG GLU ILE VAL GLY SEQRES 37 A 596 VAL VAL GLU PRO VAL PRO HIS ASP GLU THR TYR CYS ASP SEQRES 38 A 596 PRO ALA SER LEU PHE HIS VAL ALA ASN ASP TYR SER PHE SEQRES 39 A 596 ILE ARG TYR TYR THR ARG THR ILE PHE GLU PHE GLN PHE SEQRES 40 A 596 HIS GLU ALA LEU CYS ARG ILE ALA GLN HIS ASN GLY PRO SEQRES 41 A 596 LEU HIS LYS CYS ASP ILE SER ASN SER THR ASP ALA GLY SEQRES 42 A 596 LYS LYS LEU HIS GLN MET LEU SER VAL GLY LYS SER GLN SEQRES 43 A 596 ALA TRP THR LYS THR LEU GLU ASP ILE VAL ASP SER ARG SEQRES 44 A 596 ASN MET ASP VAL GLY PRO LEU LEU ARG TYR PHE LYS PRO SEQRES 45 A 596 LEU TYR THR TRP LEU GLN GLU GLN ASN ARG LYS SER TYR SEQRES 46 A 596 VAL GLY TRP ASN THR ASP TRP SER PRO TYR ALA HET NAG B 1 14 HET NAG B 2 14 HET NAG A 701 14 HET NAG A 702 14 HET ZN A 705 1 HET NAG A 706 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM ZN ZINC ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG 5(C8 H15 N O6) FORMUL 5 ZN ZN 2+ HELIX 1 AA1 THR A 20 ASN A 53 1 34 HELIX 2 AA2 ASP A 56 ASN A 82 1 27 HELIX 3 AA3 ASN A 90 GLN A 101 1 12 HELIX 4 AA4 SER A 109 THR A 129 1 21 HELIX 5 AA5 PRO A 146 SER A 155 1 10 HELIX 6 AA6 ASP A 157 TYR A 194 1 38 HELIX 7 AA7 ASP A 198 ARG A 205 1 8 HELIX 8 AA8 SER A 218 MET A 249 1 32 HELIX 9 AA9 HIS A 265 LEU A 267 5 3 HELIX 10 AB1 TRP A 275 TYR A 279 5 5 HELIX 11 AB2 VAL A 293 GLN A 300 1 8 HELIX 12 AB3 ASP A 303 SER A 317 1 15 HELIX 13 AB4 THR A 324 SER A 331 1 8 HELIX 14 AB5 MET A 366 TYR A 385 1 20 HELIX 15 AB6 PRO A 389 ARG A 393 5 5 HELIX 16 AB7 GLY A 399 ALA A 413 1 15 HELIX 17 AB8 THR A 414 THR A 420 1 7 HELIX 18 AB9 ASP A 431 VAL A 447 1 17 HELIX 19 AC1 THR A 449 GLY A 466 1 18 HELIX 20 AC2 PRO A 469 GLU A 471 5 3 HELIX 21 AC3 GLU A 472 ILE A 484 1 13 HELIX 22 AC4 CYS A 498 LEU A 503 5 6 HELIX 23 AC5 HIS A 505 ASP A 509 5 5 HELIX 24 AC6 ILE A 513 ALA A 533 1 21 HELIX 25 AC7 SER A 547 SER A 559 1 13 HELIX 26 AC8 ALA A 565 ASP A 575 1 11 HELIX 27 AC9 VAL A 581 ASN A 599 1 19 HELIX 28 AD1 ARG A 600 SER A 602 5 3 SHEET 1 AA1 2 LYS A 131 CYS A 133 0 SHEET 2 AA1 2 CYS A 141 LEU A 143 -1 O LEU A 142 N VAL A 132 SHEET 1 AA2 2 LEU A 262 PRO A 263 0 SHEET 2 AA2 2 VAL A 487 VAL A 488 1 O VAL A 488 N LEU A 262 SHEET 1 AA3 2 THR A 347 ASP A 350 0 SHEET 2 AA3 2 PHE A 356 LYS A 359 -1 O LYS A 359 N THR A 347 SSBOND 1 CYS A 133 CYS A 141 1555 1555 2.03 SSBOND 2 CYS A 344 CYS A 361 1555 1555 2.03 SSBOND 3 CYS A 530 CYS A 542 1555 1555 2.03 LINK ND2 ASN A 53 C1 NAG A 701 1555 1555 1.44 LINK ND2 ASN A 90 C1 NAG A 702 1555 1555 1.44 LINK ND2 ASN A 329 C1 NAG A 706 1555 1555 1.44 LINK ND2 ASN A 546 C1 NAG B 1 1555 1555 1.44 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.37 LINK NE2 HIS A 374 ZN ZN A 705 1555 1555 2.10 LINK NE2 HIS A 378 ZN ZN A 705 1555 1555 2.10 LINK OE2 GLU A 402 ZN ZN A 705 1555 1555 2.00 CISPEP 1 GLU A 145 PRO A 146 0 -2.21 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