HEADER VIRAL PROTEIN/IMMUNE SYSTEM 17-JUN-21 7N9A TITLE POTENT NEUTRALIZING NANOBODIES RESIST CONVERGENT CIRCULATING VARIANTS TITLE 2 OF SARS-COV-2 BY TARGETING NOVEL AND CONSERVED EPITOPES-COVS RBD WITH TITLE 3 NB21 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY NB21; 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 FRAGMENT: RECEPTOR BINDING DOMAIN; COMPND 9 SYNONYM: SPIKE GLYCOPROTEIN; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_TAXID: 9844; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 9 2; SOURCE 10 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2, COVID-19 VIRUS; SOURCE 11 ORGANISM_TAXID: 2697049; SOURCE 12 GENE: S, 2; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS COVS NB21 NANOBODY, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM KEYWDS 2 COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR D.SUN,C.ZHANG,Y.SHI REVDAT 1 04-AUG-21 7N9A 0 JRNL AUTH D.SUN,Y.SHI,C.ZHANG,W.HUANG,S.D.DINA JRNL TITL POTENT NEUTRALIZING NANOBODIES RESIST CONVERGENT CIRCULATING JRNL TITL 2 VARIANTS OF SARS-COV-2 BY TARGETING NOVEL AND CONSERVED JRNL TITL 3 EPITOPES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.50 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) : 3.500 REMARK 3 NUMBER OF PARTICLES : 97000 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 7N9A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1000256095. 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 SPIKE S WITH REMARK 245 NANOBODY NB21; SARS-COV-2 SPIKE REMARK 245 PROTEIN RECEPTOR-BINDING DOMAIN; REMARK 245 NANOBODY NB21 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 : 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 : FEI FALCON III (4K X 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) : 6000.00 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 THR A 101 OH TYR E 489 2.13 REMARK 500 OD1 ASN E 448 ND2 ASN E 450 2.18 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 CYS A 22 CA - CB - SG ANGL. DEV. = 11.6 DEGREES REMARK 500 PRO E 499 CA - N - CD ANGL. DEV. = -9.0 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 ASP A 98 -108.59 -110.82 REMARK 500 THR A 101 -101.51 -114.65 REMARK 500 PRO E 337 45.57 -80.41 REMARK 500 ASN E 422 -69.01 -132.32 REMARK 500 LEU E 441 -63.07 -94.51 REMARK 500 LEU E 455 -71.13 -128.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-24253 RELATED DB: EMDB REMARK 900 POTENT NEUTRALIZING NANOBODIES RESIST CONVERGENT CIRCULATING REMARK 900 VARIANTS OF SARS-COV-2 BY TARGETING NOVEL AND CONSERVED EPITOPES- REMARK 900 COVS RBD WITH NB21 DBREF 7N9A A 1 117 PDB 7N9A 7N9A 1 117 DBREF 7N9A E 334 528 UNP P0DTC2 SPIKE_SARS2 334 528 SEQRES 1 A 117 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 117 ALA GLY GLY SER LEU ARG LEU SER CYS ALA VAL SER GLY SEQRES 3 A 117 LEU GLY ALA HIS ARG VAL GLY TRP PHE ARG ARG ALA PRO SEQRES 4 A 117 GLY LYS GLU ARG GLU PHE VAL ALA ALA ILE GLY ALA ASN SEQRES 5 A 117 GLY GLY ASN THR ASN TYR LEU ASP SER VAL LYS GLY ARG SEQRES 6 A 117 PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR ILE TYR SEQRES 7 A 117 LEU GLN MET ASN SER LEU LYS PRO GLN ASP THR ALA VAL SEQRES 8 A 117 TYR TYR CYS ALA ALA ARG ASP ILE GLU THR ALA GLU TYR SEQRES 9 A 117 THR TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SER SEQRES 1 E 195 ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR ARG SEQRES 2 E 195 PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SER SEQRES 3 E 195 ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER ALA SEQRES 4 E 195 SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO THR SEQRES 5 E 195 LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA ASP SEQRES 6 E 195 SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE ALA SEQRES 7 E 195 PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR LYS SEQRES 8 E 195 LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP ASN SEQRES 9 E 195 SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR ASN SEQRES 10 E 195 TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS PRO SEQRES 11 E 195 PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA GLY SEQRES 12 E 195 SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS TYR SEQRES 13 E 195 PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN GLY SEQRES 14 E 195 VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER PHE SEQRES 15 E 195 GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO LYS HELIX 1 AA1 LYS A 85 THR A 89 5 5 HELIX 2 AA2 PRO E 337 ASN E 343 1 7 HELIX 3 AA3 ASP E 364 SER E 371 1 8 HELIX 4 AA4 PRO E 384 LEU E 390 5 7 HELIX 5 AA5 ASP E 405 ARG E 408 5 4 HELIX 6 AA6 GLY E 416 ASN E 422 1 7 HELIX 7 AA7 GLY E 502 TYR E 505 5 4 SHEET 1 AA1 4 LEU A 4 SER A 7 0 SHEET 2 AA1 4 ARG A 19 VAL A 24 -1 O ALA A 23 N VAL A 5 SHEET 3 AA1 4 THR A 76 MET A 81 -1 O LEU A 79 N LEU A 20 SHEET 4 AA1 4 PHE A 66 ARG A 70 -1 N THR A 67 O GLN A 80 SHEET 1 AA2 5 LEU A 11 GLN A 13 0 SHEET 2 AA2 5 THR A 111 SER A 116 1 O THR A 114 N VAL A 12 SHEET 3 AA2 5 ALA A 90 ALA A 96 -1 N TYR A 92 O THR A 111 SHEET 4 AA2 5 VAL A 32 ARG A 37 -1 N PHE A 35 O TYR A 93 SHEET 5 AA2 5 GLU A 44 ILE A 49 -1 O ALA A 47 N TRP A 34 SHEET 1 AA3 4 LEU A 11 GLN A 13 0 SHEET 2 AA3 4 THR A 111 SER A 116 1 O THR A 114 N VAL A 12 SHEET 3 AA3 4 ALA A 90 ALA A 96 -1 N TYR A 92 O THR A 111 SHEET 4 AA3 4 TYR A 106 TRP A 107 -1 O TYR A 106 N ALA A 96 SHEET 1 AA4 5 ASN E 354 ILE E 358 0 SHEET 2 AA4 5 ASN E 394 ARG E 403 -1 O ALA E 397 N LYS E 356 SHEET 3 AA4 5 PRO E 507 GLU E 516 -1 O VAL E 510 N PHE E 400 SHEET 4 AA4 5 GLY E 431 ASN E 437 -1 N ILE E 434 O VAL E 511 SHEET 5 AA4 5 THR E 376 TYR E 380 -1 N TYR E 380 O GLY E 431 SHEET 1 AA5 2 LEU E 452 ARG E 454 0 SHEET 2 AA5 2 LEU E 492 SER E 494 -1 O GLN E 493 N TYR E 453 SSBOND 1 CYS A 22 CYS A 94 1555 1555 2.05 SSBOND 2 CYS E 336 CYS E 361 1555 1555 2.03 SSBOND 3 CYS E 379 CYS E 432 1555 1555 2.03 SSBOND 4 CYS E 391 CYS E 525 1555 1555 2.04 SSBOND 5 CYS E 480 CYS E 488 1555 1555 2.04 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