HEADER VIRAL PROTEIN 04-JUN-26 27KF TITLE CRYO-EM STRUCTURE OF TUNDRA SWAN ACE2 COMPLEXED WITH SARS-COV-2 RBD COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUNDRA SWAN ACE2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SPIKE PROTEIN S1; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CYGNUS COLUMBIANUS; SOURCE 3 ORGANISM_TAXID: 110926; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 8 2; SOURCE 9 ORGANISM_TAXID: 2697049; SOURCE 10 GENE: S, 2; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS CRYO-EM STRUCTURE, TUNDRA SWAN ACE2, SARS-COV-2, RBD, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR F.G.GAO,S.LIU REVDAT 1 17-JUN-26 27KF 0 JRNL AUTH F.G.GAO,S.LIU JRNL TITL CRYO-EM STRUCTURE OF TUNDRA SWAN ACE2 COMPLEXED WITH JRNL TITL 2 SARS-COV-2 RBD JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : RELION, PHENIX, RELION 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) : 3.400 REMARK 3 NUMBER OF PARTICLES : 112777 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 27KF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 08-JUN-26. REMARK 100 THE DEPOSITION ID IS D_1300075166. 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 : CRYO-EM STRUCTURE OF TUNDRA REMARK 245 SWAN ACE2 COMPLEXED WITH SARS- REMARK 245 COV-2 RBD 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 : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOCONTINUUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 5000.00 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) : 167.00 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: 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 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 A 123 CA - CB - SG ANGL. DEV. = 8.5 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 THR A 117 -168.84 -125.06 REMARK 500 PRO A 128 86.69 7.37 REMARK 500 ALA A 187 -7.10 -59.70 REMARK 500 THR A 317 -166.77 -123.86 REMARK 500 LYS A 324 128.21 -38.36 REMARK 500 CYS A 327 40.31 -102.94 REMARK 500 LYS A 346 -168.02 -126.47 REMARK 500 PRO A 372 172.67 -58.97 REMARK 500 GLU A 455 27.92 -140.17 REMARK 500 ASP B 32 59.43 -96.56 REMARK 500 TYR B 117 33.13 -97.65 REMARK 500 PHE B 124 130.35 -37.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-81218 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF TUNDRA SWAN ACE2 COMPLEXED WITH SARS-COV-2 RBD DBREF 27KF A 1 597 PDB 27KF 27KF 1 597 DBREF 27KF B 1 195 UNP P0DTC2 SPIKE_SARS2 333 527 SEQADV 27KF THR B 85 UNP P0DTC2 LYS 417 VARIANT SEQADV 27KF LYS B 152 UNP P0DTC2 GLU 484 VARIANT SEQADV 27KF TYR B 169 UNP P0DTC2 ASN 501 VARIANT SEQRES 1 A 597 GLN ASP VAL THR ASN GLN ALA GLN MET PHE LEU ALA GLU SEQRES 2 A 597 PHE ASN VAL ARG ALA GLU ASP ILE SER TYR GLU SER SER SEQRES 3 A 597 LEU ALA SER TRP ASN TYR ASN THR ASN ILE THR GLU GLU SEQRES 4 A 597 THR ALA THR LYS MET ASN GLU VAL GLY ALA LYS TRP SER SEQRES 5 A 597 ALA PHE TYR GLU GLU ALA SER LYS ASN ALA SER SER PHE SEQRES 6 A 597 LEU LEU SER ASP ILE GLN ASP PRO LEU ILE ARG LEU GLN SEQRES 7 A 597 ILE GLN SER LEU GLN ASP ARG GLY SER SER VAL LEU SER SEQRES 8 A 597 PRO GLU LYS TYR SER ARG LEU SER THR VAL LEU ASN THR SEQRES 9 A 597 MET SER THR ILE TYR SER THR GLY THR VAL CYS LYS THR SEQRES 10 A 597 THR GLU PRO PHE ASP CYS MET VAL LEU GLU PRO GLY LEU SEQRES 11 A 597 ASP SER ILE MET ALA TYR SER ILE ASP TYR HIS GLU ARG SEQRES 12 A 597 LEU TRP ALA TRP GLU ALA TRP ARG ALA ASP VAL GLY ARG SEQRES 13 A 597 MET MET ARG PRO LEU TYR GLU GLU TYR VAL GLU LEU LYS SEQRES 14 A 597 ASN GLU ALA ALA LYS LEU ASN SER TYR ALA ASP TYR GLY SEQRES 15 A 597 ASP TYR TRP ARG ALA ASN TYR GLU ALA ASP TYR PRO GLU SEQRES 16 A 597 GLU TYR LYS TYR SER ARG ASP GLN LEU VAL GLN ASP VAL SEQRES 17 A 597 GLU LYS THR PHE GLU GLN ILE LYS PRO LEU TYR GLN GLN SEQRES 18 A 597 LEU HIS ALA TYR VAL ARG HIS ARG LEU GLU GLN ALA TYR SEQRES 19 A 597 GLY SER GLN PHE ILE SER SER THR GLY CYS LEU PRO ALA SEQRES 20 A 597 HIS LEU LEU GLY ASP MET TRP GLY ARG PHE TRP THR ASN SEQRES 21 A 597 LEU TYR SER LEU THR VAL PRO TYR PRO ALA LYS PRO ASN SEQRES 22 A 597 ILE ASP VAL THR ASP ALA MET VAL GLN LYS ASN TRP ASP SEQRES 23 A 597 ALA MET LYS ILE PHE LYS ALA ALA GLU ALA PHE PHE SER SEQRES 24 A 597 SER ILE GLY LEU TYR ASN MET THR GLU GLY PHE TRP LYS SEQRES 25 A 597 ASN SER MET LEU THR GLU PRO THR ASP ASN ARG LYS VAL SEQRES 26 A 597 VAL CYS HIS PRO THR ALA TRP ASP MET GLY LYS ASN ASP SEQRES 27 A 597 TYR ARG ILE LYS MET CYS THR LYS VAL THR MET ASP ASP SEQRES 28 A 597 PHE LEU THR ALA HIS HIS GLU MET GLY HIS ILE GLU TYR SEQRES 29 A 597 ASP MET ALA TYR SER VAL GLN PRO PHE LEU LEU ARG ASP SEQRES 30 A 597 GLY ALA ASN GLU GLY PHE HIS GLU ALA VAL GLY GLU ILE SEQRES 31 A 597 MET SER LEU SER ALA ALA THR PRO GLN HIS LEU LYS SER SEQRES 32 A 597 LEU ASN LEU LEU GLU PRO THR PHE GLN GLU ASP GLU GLU SEQRES 33 A 597 THR GLU ILE ASN PHE LEU LEU LYS GLN ALA LEU THR ILE SEQRES 34 A 597 VAL GLY THR MET PRO PHE THR TYR MET LEU GLU LYS TRP SEQRES 35 A 597 ARG TRP MET VAL PHE ARG GLY GLU ILE THR LYS GLN GLU SEQRES 36 A 597 TRP THR LYS ARG TRP TRP GLU MET LYS ARG ASP ILE VAL SEQRES 37 A 597 GLY VAL VAL GLU PRO VAL PRO HIS ASP GLU THR TYR CYS SEQRES 38 A 597 ASP PRO ALA ALA LEU PHE HIS VAL ALA ASN ASP TYR SER SEQRES 39 A 597 PHE ILE ARG TYR TYR THR ARG THR ILE TYR GLN PHE GLN SEQRES 40 A 597 PHE HIS GLU ALA LEU CYS LYS ALA ALA LYS HIS THR GLY SEQRES 41 A 597 PRO LEU HIS THR CYS ASP ILE THR ASN SER THR ALA ALA SEQRES 42 A 597 GLY GLY ASN LEU ARG GLY LEU LEU GLU LEU GLY ARG SER SEQRES 43 A 597 LYS PRO TRP THR GLN ALA LEU GLU ASN LEU THR GLY GLU SEQRES 44 A 597 LYS TYR MET ASN ALA THR PRO LEU LEU HIS TYR PHE GLU SEQRES 45 A 597 PRO LEU PHE ASN TRP LEU GLN LYS ASN ASN SER GLY ARG SEQRES 46 A 597 TYR ILE GLY TRP ASN THR ASP TRP THR PRO TYR SER SEQRES 1 B 195 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 B 195 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 B 195 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 B 195 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 B 195 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 B 195 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 B 195 ALA PRO GLY GLN THR GLY THR ILE ALA ASP TYR ASN TYR SEQRES 8 B 195 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 B 195 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 B 195 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 B 195 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 B 195 GLY SER THR PRO CYS ASN GLY VAL LYS GLY PHE ASN CYS SEQRES 13 B 195 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR TYR SEQRES 14 B 195 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 B 195 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO HELIX 1 AA1 ASP A 2 THR A 34 1 33 HELIX 2 AA2 THR A 37 SER A 64 1 28 HELIX 3 AA3 ASP A 72 GLN A 83 1 12 HELIX 4 AA4 ARG A 85 LEU A 90 5 6 HELIX 5 AA5 SER A 91 THR A 111 1 21 HELIX 6 AA6 GLU A 119 CYS A 123 5 5 HELIX 7 AA7 GLY A 129 SER A 137 1 9 HELIX 8 AA8 ASP A 139 ASN A 176 1 38 HELIX 9 AA9 ASP A 180 ALA A 187 1 8 HELIX 10 AB1 SER A 200 GLY A 235 1 36 HELIX 11 AB2 HIS A 248 LEU A 250 5 3 HELIX 12 AB3 PHE A 257 ASN A 260 5 4 HELIX 13 AB4 LEU A 261 VAL A 266 1 6 HELIX 14 AB5 VAL A 276 LYS A 283 1 8 HELIX 15 AB6 ASP A 286 GLY A 302 1 17 HELIX 16 AB7 THR A 307 SER A 314 1 8 HELIX 17 AB8 THR A 348 SER A 369 1 22 HELIX 18 AB9 VAL A 370 GLN A 371 5 2 HELIX 19 AC1 PRO A 372 ARG A 376 5 5 HELIX 20 AC2 GLY A 382 ALA A 395 1 14 HELIX 21 AC3 THR A 397 LEU A 404 1 8 HELIX 22 AC4 ASP A 414 ILE A 429 1 16 HELIX 23 AC5 THR A 432 ARG A 448 1 17 HELIX 24 AC6 THR A 452 GLN A 454 5 3 HELIX 25 AC7 GLU A 455 VAL A 468 1 14 HELIX 26 AC8 CYS A 481 ALA A 485 5 5 HELIX 27 AC9 LEU A 486 ASN A 491 1 6 HELIX 28 AD1 PHE A 495 LYS A 517 1 23 HELIX 29 AD2 PRO A 521 CYS A 525 5 5 HELIX 30 AD3 SER A 530 GLY A 544 1 15 HELIX 31 AD4 PRO A 548 THR A 557 1 10 HELIX 32 AD5 ALA A 564 PHE A 571 1 8 HELIX 33 AD6 PHE A 571 ASN A 582 1 12 HELIX 34 AD7 PRO B 5 ASN B 11 1 7 HELIX 35 AD8 TYR B 33 SER B 39 1 7 HELIX 36 AD9 PRO B 52 ASN B 56 5 5 HELIX 37 AE1 GLY B 84 ASN B 90 1 7 HELIX 38 AE2 SER B 106 SER B 111 1 6 HELIX 39 AE3 GLY B 170 GLN B 174 5 5 SHEET 1 AA1 2 LEU A 245 PRO A 246 0 SHEET 2 AA1 2 VAL A 470 VAL A 471 1 O VAL A 471 N LEU A 245 SHEET 1 AA2 2 THR A 330 ASP A 333 0 SHEET 2 AA2 2 TYR A 339 LYS A 342 -1 O ARG A 340 N TRP A 332 SHEET 1 AA3 5 ASN B 22 ILE B 26 0 SHEET 2 AA3 5 VAL B 63 ILE B 70 -1 O ALA B 65 N LYS B 24 SHEET 3 AA3 5 TYR B 176 PHE B 183 -1 O VAL B 180 N ASP B 66 SHEET 4 AA3 5 GLY B 99 ASN B 105 -1 N ILE B 102 O VAL B 179 SHEET 5 AA3 5 THR B 44 TYR B 48 -1 N TYR B 48 O GLY B 99 SHEET 1 AA4 2 LEU B 120 ARG B 122 0 SHEET 2 AA4 2 LEU B 160 SER B 162 -1 O GLN B 161 N TYR B 121 SSBOND 1 CYS A 115 CYS A 123 1555 1555 2.01 SSBOND 2 CYS A 327 CYS A 344 1555 1555 2.03 SSBOND 3 CYS A 513 CYS A 525 1555 1555 2.03 SSBOND 4 CYS B 4 CYS B 29 1555 1555 2.03 SSBOND 5 CYS B 47 CYS B 100 1555 1555 2.03 SSBOND 6 CYS B 59 CYS B 193 1555 1555 2.03 SSBOND 7 CYS B 148 CYS B 156 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 CONECT 903 967 CONECT 967 903 CONECT 2665 2807 CONECT 2807 2665 CONECT 4216 4303 CONECT 4303 4216 CONECT 4917 5124 CONECT 5124 4917 CONECT 5264 5675 CONECT 5354 6422 CONECT 5675 5264 CONECT 6066 6123 CONECT 6123 6066 CONECT 6422 5354 MASTER 147 0 0 39 11 0 0 6 6433 2 14 61 END