HEADER VIRAL PROTEIN 23-NOV-20 7B14 TITLE NANOBODY E BOUND TO SPIKE-RBD IN A LOCALIZED RECONSTRUCTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NANOBODY AGAINST SARS-COV-2; COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: CAMELUS BACTRIANUS; SOURCE 11 ORGANISM_TAXID: 9837; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SPIKE GLYCOPROTEIN, SARS-COV-2, NANOBODY, VIRAL PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR B.M.HALLBERG,H.DAS REVDAT 4 21-DEC-22 7B14 1 JRNL REVDAT 3 02-JUN-21 7B14 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 SEQADV SEQRES HELIX SHEET REVDAT 3 3 1 SSBOND LINK ATOM REVDAT 2 26-MAY-21 7B14 1 TITLE REVDAT 1 28-APR-21 7B14 0 JRNL AUTH P.A.KOENIG,H.DAS,H.LIU,B.M.KUMMERER,F.N.GOHR,L.M.JENSTER, JRNL AUTH 2 L.D.J.SCHIFFELERS,Y.M.TESFAMARIAM,M.UCHIMA,J.D.WUERTH, JRNL AUTH 3 K.GATTERDAM,N.RUETALO,M.H.CHRISTENSEN,C.I.FANDREY,S.NORMANN, JRNL AUTH 4 J.M.P.TODTMANN,S.PRITZL,L.HANKE,J.BOOS,M.YUAN,X.ZHU, JRNL AUTH 5 J.L.SCHMID-BURGK,H.KATO,M.SCHINDLER,I.A.WILSON,M.GEYER, JRNL AUTH 6 K.U.LUDWIG,B.M.HALLBERG,N.C.WU,F.I.SCHMIDT JRNL TITL STRUCTURE-GUIDED MULTIVALENT NANOBODIES BLOCK SARS-COV-2 JRNL TITL 2 INFECTION AND SUPPRESS MUTATIONAL ESCAPE JRNL REF SCIENCE V. 371 2021 JRNL REFN ESSN 1095-9203 JRNL PMID 33436526 JRNL DOI 10.1126/SCIENCE.ABE6230 REMARK 2 REMARK 2 RESOLUTION. 3.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, 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 : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT 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) : 3.790 REMARK 3 NUMBER OF PARTICLES : 38308 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 7B14 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1292112464. 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 GLYCOPROTEIN IN REMARK 245 COMPLEX WITH A NANOBODY NAMED V; REMARK 245 SPIKE GLYCOPROTEIN; NANOBODY REMARK 245 AGAINST SARS-COV-2 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 : 7.30 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) : 4900.00 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 LYS A 528 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 LEU A 518 CG CD1 CD2 REMARK 470 GLN D 1 OE1 NE2 REMARK 470 GLN D 13 CG CD OE1 NE2 REMARK 470 LYS D 64 CE NZ REMARK 470 ASN D 73 OD1 ND2 REMARK 470 LYS D 75 CE NZ REMARK 470 GLU D 85 CD OE1 OE2 REMARK 470 LYS D 105 CD CE NZ 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 OG SER D 100I OD1 ASP D 100K 2.19 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 CYS A 432 -179.40 -173.97 REMARK 500 LYS D 64 15.11 57.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-11978 RELATED DB: EMDB REMARK 900 NANOBODY E BOUND TO SPIKE-RBD IN A LOCALIZED RECONSTRUCTION. DBREF 7B14 A 333 528 UNP P0DTC2 SPIKE_SARS2 333 528 DBREF 7B14 D 1 113 PDB 7B14 7B14 1 113 SEQRES 1 A 196 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 A 196 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 A 196 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 A 196 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 A 196 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 A 196 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 A 196 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 8 A 196 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 A 196 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 A 196 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 A 196 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 A 196 GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 13 A 196 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 14 A 196 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 A 196 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY PRO SEQRES 16 A 196 LYS SEQRES 1 D 129 GLN VAL GLN LEU VAL GLU THR GLY GLY GLY PHE VAL GLN SEQRES 2 D 129 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 D 129 VAL THR LEU ASP TYR TYR ALA ILE GLY TRP PHE ARG GLN SEQRES 4 D 129 ALA PRO GLY LYS GLU ARG GLU GLY VAL SER CYS ILE GLY SEQRES 5 D 129 SER SER ASP GLY ARG THR TYR TYR SER ASP SER VAL LYS SEQRES 6 D 129 GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 D 129 VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR SEQRES 8 D 129 ALA VAL TYR TYR CYS ALA LEU THR VAL GLY THR TYR TYR SEQRES 9 D 129 SER GLY ASN TYR HIS TYR THR CYS SER ASP ASP MET ASP SEQRES 10 D 129 TYR TRP GLY LYS GLY THR GLN VAL THR VAL SER SER HET NAG A1301 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 3 NAG C8 H15 N O6 HELIX 1 AA1 ASP A 364 ASN A 370 1 7 HELIX 2 AA2 SER A 383 LEU A 387 5 5 HELIX 3 AA3 ARG A 403 ILE A 410 1 8 HELIX 4 AA4 GLY A 502 GLN A 506 5 5 HELIX 5 AA5 LYS D 83 THR D 87 5 5 SHEET 1 AA1 4 ASN A 354 ILE A 358 0 SHEET 2 AA1 4 ASN A 394 ILE A 402 -1 O ALA A 397 N LYS A 356 SHEET 3 AA1 4 TYR A 508 GLU A 516 -1 O TYR A 508 N ILE A 402 SHEET 4 AA1 4 GLY A 431 ASN A 437 -1 N CYS A 432 O LEU A 513 SHEET 1 AA2 2 LEU A 452 ARG A 454 0 SHEET 2 AA2 2 LEU A 492 SER A 494 -1 O GLN A 493 N TYR A 453 SHEET 1 AA3 4 GLN D 3 THR D 7 0 SHEET 2 AA3 4 LEU D 18 SER D 25 -1 O SER D 21 N THR D 7 SHEET 3 AA3 4 THR D 77 MET D 82 -1 O LEU D 80 N LEU D 20 SHEET 4 AA3 4 THR D 68 ASP D 72 -1 N THR D 68 O GLN D 81 SHEET 1 AA4 5 THR D 57 TYR D 59 0 SHEET 2 AA4 5 ARG D 45 GLY D 52 -1 N CYS D 50 O TYR D 58 SHEET 3 AA4 5 TYR D 32 GLN D 39 -1 N ILE D 34 O ILE D 51 SHEET 4 AA4 5 ALA D 88 VAL D 96 -1 O VAL D 89 N GLN D 39 SHEET 5 AA4 5 THR D 107 VAL D 109 -1 O THR D 107 N TYR D 90 SHEET 1 AA5 2 THR D 98 TYR D 100 0 SHEET 2 AA5 2 ASN D 100C HIS D 100E-1 O ASN D 100C N TYR D 100 SSBOND 1 CYS A 336 CYS A 361 1555 1555 2.03 SSBOND 2 CYS A 379 CYS A 432 1555 1555 2.03 SSBOND 3 CYS A 391 CYS A 525 1555 1555 2.03 SSBOND 4 CYS A 480 CYS A 488 1555 1555 2.03 SSBOND 5 CYS D 22 CYS D 92 1555 1555 2.03 SSBOND 6 CYS D 50 CYS D 100H 1555 1555 2.03 LINK ND2 ASN A 343 C1 NAG A1301 1555 1555 1.45 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