HEADER PROTEIN BINDING 15-DEC-22 8HRL TITLE SARS-COV-2 DELTA S-RBD-ACE2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROCESSED ANGIOTENSIN-CONVERTING ENZYME 2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SPIKE PROTEIN S1; COMPND 7 CHAIN: E; COMPND 8 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: ACE2, UNQ868/PRO1885; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 10 2; SOURCE 11 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 12 ORGANISM_TAXID: 2697049; SOURCE 13 GENE: S, 2; SOURCE 14 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS SARS-COV-2, DELTA, RBD, ACE2, PROTEIN BINDING EXPDTA ELECTRON MICROSCOPY AUTHOR J.XU,F.MENG,N.LIU,H.W.WANG REVDAT 1 20-DEC-23 8HRL 0 JRNL AUTH L.ZHENG,J.XU,W.WANG,X.GAO,N.LIU,H.W.WANG,H.L.PENG JRNL TITL SELF-ASSEMBLED MONOLAYERS GUIDED FREE-STANDING JRNL TITL 2 ATOMIC-CRYSTAL/MOLECULE SUPERSTRUCTURE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.80 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) : 2.800 REMARK 3 NUMBER OF PARTICLES : 224616 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 8HRL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 06-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1300034174. 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 : SARS-COV-2 DELTA S-RBD-ACE2 REMARK 245 COMPLEX 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 : ON GRAPHENE MEMBRANES 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) : 1200.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1500.00 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: A, E 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O PHE A 327 OG SER A 331 2.12 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 PRO A 258 N - CD - CG ANGL. DEV. = -9.7 DEGREES REMARK 500 PRO E 499 CA - N - CD ANGL. DEV. = -12.2 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 140 48.20 -89.05 REMARK 500 LEU A 143 -166.40 -77.96 REMARK 500 LEU A 144 -61.28 -95.36 REMARK 500 PRO A 146 53.33 -93.34 REMARK 500 ASN A 194 30.06 -96.81 REMARK 500 PRO A 321 -177.45 -67.61 REMARK 500 PRO A 336 44.01 -82.60 REMARK 500 ASP A 509 70.81 36.66 REMARK 500 LYS A 534 64.57 61.79 REMARK 500 ASN A 599 32.27 -99.22 REMARK 500 ASP E 405 34.49 -83.20 REMARK 500 SER E 438 45.72 -145.88 REMARK 500 ASP E 442 31.01 -93.05 REMARK 500 TYR E 449 41.47 -102.29 REMARK 500 ASN E 481 79.88 -101.92 REMARK 500 HIS E 519 32.57 -93.22 REMARK 500 THR E 523 10.03 -140.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-34977 RELATED DB: EMDB REMARK 900 SARS-COV-2 DELTA S-RBD-ACE2 DBREF 8HRL A 19 615 UNP Q9BYF1 ACE2_HUMAN 19 615 DBREF 8HRL E 333 526 UNP P0DTC2 SPIKE_SARS2 333 526 SEQADV 8HRL ARG E 452 UNP P0DTC2 LEU 452 VARIANT SEQADV 8HRL LYS E 478 UNP P0DTC2 THR 478 VARIANT SEQRES 1 A 597 SER THR ILE GLU GLU GLN ALA LYS THR PHE LEU ASP LYS SEQRES 2 A 597 PHE ASN HIS GLU ALA GLU ASP LEU PHE TYR GLN SER SER SEQRES 3 A 597 LEU ALA SER TRP ASN TYR ASN THR ASN ILE THR GLU GLU SEQRES 4 A 597 ASN VAL GLN ASN MET ASN ASN ALA GLY ASP LYS TRP SER SEQRES 5 A 597 ALA PHE LEU LYS GLU GLN SER THR LEU ALA GLN MET TYR SEQRES 6 A 597 PRO LEU GLN GLU ILE GLN ASN LEU THR VAL LYS LEU GLN SEQRES 7 A 597 LEU GLN ALA LEU GLN GLN ASN GLY SER SER VAL LEU SER SEQRES 8 A 597 GLU ASP LYS SER LYS ARG LEU ASN THR ILE LEU ASN THR SEQRES 9 A 597 MET SER THR ILE TYR SER THR GLY LYS VAL CYS ASN PRO SEQRES 10 A 597 ASP ASN PRO GLN GLU CYS LEU LEU LEU GLU PRO GLY LEU SEQRES 11 A 597 ASN GLU ILE MET ALA ASN SER LEU ASP TYR ASN GLU ARG SEQRES 12 A 597 LEU TRP ALA TRP GLU SER TRP ARG SER GLU VAL GLY LYS SEQRES 13 A 597 GLN LEU ARG PRO LEU TYR GLU GLU TYR VAL VAL LEU LYS SEQRES 14 A 597 ASN GLU MET ALA ARG ALA ASN HIS TYR GLU ASP TYR GLY SEQRES 15 A 597 ASP TYR TRP ARG GLY ASP TYR GLU VAL ASN GLY VAL ASP SEQRES 16 A 597 GLY TYR ASP TYR SER ARG GLY GLN LEU ILE GLU ASP VAL SEQRES 17 A 597 GLU HIS THR PHE GLU GLU ILE LYS PRO LEU TYR GLU HIS SEQRES 18 A 597 LEU HIS ALA TYR VAL ARG ALA LYS LEU MET ASN ALA TYR SEQRES 19 A 597 PRO SER TYR ILE SER PRO ILE GLY CYS LEU PRO ALA HIS SEQRES 20 A 597 LEU LEU GLY ASP MET TRP GLY ARG PHE TRP THR ASN LEU SEQRES 21 A 597 TYR SER LEU THR VAL PRO PHE GLY GLN LYS PRO ASN ILE SEQRES 22 A 597 ASP VAL THR ASP ALA MET VAL ASP GLN ALA TRP ASP ALA SEQRES 23 A 597 GLN ARG ILE PHE LYS GLU ALA GLU LYS PHE PHE VAL SER SEQRES 24 A 597 VAL GLY LEU PRO ASN MET THR GLN GLY PHE TRP GLU ASN SEQRES 25 A 597 SER MET LEU THR ASP PRO GLY ASN VAL GLN LYS ALA VAL SEQRES 26 A 597 CYS HIS PRO THR ALA TRP ASP LEU GLY LYS GLY ASP PHE SEQRES 27 A 597 ARG ILE LEU MET CYS THR LYS VAL THR MET ASP ASP PHE SEQRES 28 A 597 LEU THR ALA HIS HIS GLU MET GLY HIS ILE GLN TYR ASP SEQRES 29 A 597 MET ALA TYR ALA ALA GLN PRO PHE LEU LEU ARG ASN GLY SEQRES 30 A 597 ALA ASN GLU GLY PHE HIS GLU ALA VAL GLY GLU ILE MET SEQRES 31 A 597 SER LEU SER ALA ALA THR PRO LYS HIS LEU LYS SER ILE SEQRES 32 A 597 GLY LEU LEU SER PRO ASP PHE GLN GLU ASP ASN GLU THR SEQRES 33 A 597 GLU ILE ASN PHE LEU LEU LYS GLN ALA LEU THR ILE VAL SEQRES 34 A 597 GLY THR LEU PRO PHE THR TYR MET LEU GLU LYS TRP ARG SEQRES 35 A 597 TRP MET VAL PHE LYS GLY GLU ILE PRO LYS ASP GLN TRP SEQRES 36 A 597 MET LYS LYS TRP TRP GLU MET LYS ARG GLU ILE VAL GLY SEQRES 37 A 597 VAL VAL GLU PRO VAL PRO HIS ASP GLU THR TYR CYS ASP SEQRES 38 A 597 PRO ALA SER LEU PHE HIS VAL SER ASN ASP TYR SER PHE SEQRES 39 A 597 ILE ARG TYR TYR THR ARG THR LEU TYR GLN PHE GLN PHE SEQRES 40 A 597 GLN GLU ALA LEU CYS GLN ALA ALA LYS HIS GLU GLY PRO SEQRES 41 A 597 LEU HIS LYS CYS ASP ILE SER ASN SER THR GLU ALA GLY SEQRES 42 A 597 GLN LYS LEU PHE ASN MET LEU ARG LEU GLY LYS SER GLU SEQRES 43 A 597 PRO TRP THR LEU ALA LEU GLU ASN VAL VAL GLY ALA LYS SEQRES 44 A 597 ASN MET ASN VAL ARG PRO LEU LEU ASN TYR PHE GLU PRO SEQRES 45 A 597 LEU PHE THR TRP LEU LYS ASP GLN ASN LYS ASN SER PHE SEQRES 46 A 597 VAL GLY TRP SER THR ASP TRP SER PRO TYR ALA ASP SEQRES 1 E 194 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 E 194 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 E 194 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 E 194 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 E 194 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 E 194 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 E 194 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 8 E 194 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 E 194 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 E 194 ASN TYR ARG TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 E 194 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 E 194 GLY SER LYS PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 13 E 194 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 14 E 194 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 E 194 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY HELIX 1 AA1 THR A 20 ASN A 53 1 34 HELIX 2 AA2 GLN A 60 ALA A 80 1 21 HELIX 3 AA3 GLN A 81 TYR A 83 5 3 HELIX 4 AA4 ASN A 90 ALA A 99 1 10 HELIX 5 AA5 ASN A 103 LEU A 108 5 6 HELIX 6 AA6 SER A 109 THR A 129 1 21 HELIX 7 AA7 TYR A 158 VAL A 172 1 15 HELIX 8 AA8 LEU A 176 ASN A 194 1 19 HELIX 9 AA9 ASP A 198 ARG A 204 1 7 HELIX 10 AB1 GLY A 220 MET A 249 1 30 HELIX 11 AB2 HIS A 265 LEU A 267 5 3 HELIX 12 AB3 TRP A 275 TYR A 279 5 5 HELIX 13 AB4 VAL A 293 GLN A 300 1 8 HELIX 14 AB5 ASP A 303 VAL A 318 1 16 HELIX 15 AB6 THR A 324 SER A 331 1 8 HELIX 16 AB7 MET A 366 TYR A 385 1 20 HELIX 17 AB8 PRO A 389 ARG A 393 5 5 HELIX 18 AB9 PHE A 400 GLY A 405 1 6 HELIX 19 AC1 GLU A 406 ALA A 413 1 8 HELIX 20 AC2 THR A 414 GLY A 422 1 9 HELIX 21 AC3 ASP A 431 VAL A 447 1 17 HELIX 22 AC4 THR A 449 GLY A 466 1 18 HELIX 23 AC5 PRO A 469 ASP A 471 5 3 HELIX 24 AC6 GLN A 472 VAL A 485 1 14 HELIX 25 AC7 ASP A 499 SER A 502 5 4 HELIX 26 AC8 LEU A 503 ASN A 508 1 6 HELIX 27 AC9 ILE A 513 ALA A 533 1 21 HELIX 28 AD1 PRO A 538 CYS A 542 5 5 HELIX 29 AD2 SER A 547 ARG A 559 1 13 HELIX 30 AD3 PRO A 565 GLY A 575 1 11 HELIX 31 AD4 VAL A 581 PHE A 588 1 8 HELIX 32 AD5 PHE A 588 ASN A 599 1 12 HELIX 33 AD6 PHE E 338 ASN E 343 1 6 HELIX 34 AD7 TYR E 365 ASN E 370 1 6 HELIX 35 AD8 THR E 385 ASP E 389 5 5 HELIX 36 AD9 ARG E 403 ILE E 410 5 8 SHEET 1 AA1 2 LEU A 262 PRO A 263 0 SHEET 2 AA1 2 VAL A 487 VAL A 488 1 O VAL A 488 N LEU A 262 SHEET 1 AA2 2 TRP A 349 GLY A 352 0 SHEET 2 AA2 2 ASP A 355 ARG A 357 -1 O ASP A 355 N LEU A 351 SHEET 1 AA3 5 ASN E 354 ILE E 358 0 SHEET 2 AA3 5 ASN E 394 ILE E 402 -1 O VAL E 395 N ILE E 358 SHEET 3 AA3 5 TYR E 508 GLU E 516 -1 O TYR E 508 N ILE E 402 SHEET 4 AA3 5 CYS E 432 ASN E 437 -1 N ILE E 434 O VAL E 511 SHEET 5 AA3 5 THR E 376 CYS E 379 -1 N THR E 376 O ALA E 435 SHEET 1 AA4 2 ARG E 452 ARG E 454 0 SHEET 2 AA4 2 LEU E 492 SER E 494 -1 O GLN E 493 N TYR E 453 SHEET 1 AA5 2 TYR E 473 GLN E 474 0 SHEET 2 AA5 2 CYS E 488 TYR E 489 -1 O TYR E 489 N TYR E 473 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 SSBOND 4 CYS E 336 CYS E 361 1555 1555 2.03 SSBOND 5 CYS E 379 CYS E 432 1555 1555 2.03 SSBOND 6 CYS E 391 CYS E 525 1555 1555 2.04 SSBOND 7 CYS E 480 CYS E 488 1555 1555 2.03 CISPEP 1 GLU A 145 PRO A 146 0 4.37 CISPEP 2 LYS E 478 PRO E 479 0 -4.83 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