HEADER VIRAL PROTEIN/IMMUNE SYSTEM 06-APR-21 7MEJ TITLE CRYOEM STRUCTURE OF SARS-COV-2 RBD IN COMPLEX WITH NANOBODIES NB21 AND TITLE 2 NB36 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: R; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: NANOBODY NB36; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_COMMON: LLAMA; SOURCE 4 ORGANISM_TAXID: 9844; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768; 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; SOURCE 11 ORGANISM_TAXID: 2697049; SOURCE 12 GENE: S, 2; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 16 MOL_ID: 3; SOURCE 17 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 18 ORGANISM_COMMON: LLAMA; SOURCE 19 ORGANISM_TAXID: 9844; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS SARS-COV-2 RECEPTOR BINDING DOMAIN NANOBODY, VIRAL PROTEIN, VIRAL KEYWDS 2 PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR W.HUANG,D.J.TAYLOR REVDAT 1 11-AUG-21 7MEJ 0 JRNL AUTH D.SUN,Z.SANG,Y.J.KIM,Y.XIANG,T.COHEN,A.K.BELFORD,A.HUET, JRNL AUTH 2 J.F.CONWAY,J.SUN,D.J.TAYLOR,D.SCHNEIDMAN-DUHOVNY,C.ZHANG, JRNL AUTH 3 W.HUANG,Y.SHI JRNL TITL POTENT NEUTRALIZING NANOBODIES RESIST CONVERGENT CIRCULATING JRNL TITL 2 VARIANTS OF SARS-COV-2 BY TARGETING DIVERSE AND CONSERVED JRNL TITL 3 EPITOPES JRNL REF NAT COMMUN V. 12 4676 2021 JRNL REFN ESSN 2041-1723 JRNL DOI 10.1038/S41467-021-24963-3 REMARK 2 REMARK 2 RESOLUTION. 3.55 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) : 3.550 REMARK 3 NUMBER OF PARTICLES : 154955 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 7MEJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-21. REMARK 100 THE DEPOSITION ID IS D_1000256071. 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 : CRYOEM MAP OF SARS-COV-2 RBD IN REMARK 245 COMPLEX WITH NB21 AND NB105 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 : 7.40 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 (6K 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) : 6040.00 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, R, 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 LEU A 11 CG CD1 CD2 REMARK 470 GLN A 13 CG CD OE1 NE2 REMARK 470 LYS A 41 CG CD CE NZ REMARK 470 GLU A 42 CG CD OE1 OE2 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 OG1 THR B 68 O MET B 82 2.05 REMARK 500 NH2 ARG A 36 O VAL A 91 2.08 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 R 379 CA - CB - SG 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 SER A 25 52.87 -91.12 REMARK 500 ALA A 29 44.40 -140.65 REMARK 500 PRO A 39 73.72 -69.72 REMARK 500 VAL A 46 -62.33 -121.22 REMARK 500 MET A 81 38.07 71.71 REMARK 500 PRO A 86 46.88 -76.03 REMARK 500 ASP A 98 -9.50 -53.85 REMARK 500 GLU A 103 -40.15 -132.77 REMARK 500 CYS R 361 -179.67 -170.14 REMARK 500 PHE R 377 115.67 -161.36 REMARK 500 LYS R 458 -39.23 -132.75 REMARK 500 SER R 459 -179.72 -176.63 REMARK 500 GLU R 465 142.76 -170.09 REMARK 500 THR R 500 37.07 -98.10 REMARK 500 SER B 30 36.65 -98.45 REMARK 500 MET B 34 -174.42 -170.22 REMARK 500 SER B 52 -3.93 70.84 REMARK 500 TRP B 52A -169.96 -166.58 REMARK 500 LYS B 75 14.13 59.49 REMARK 500 LEU B 82C -169.15 -78.85 REMARK 500 GLU B 85 60.39 60.90 REMARK 500 SER B 98 147.49 -173.69 REMARK 500 TYR B 102 26.71 -140.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-23788 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-23782 RELATED DB: EMDB REMARK 900 RELATED ID: EMD-23790 RELATED DB: EMDB REMARK 900 CRYOEM STRUCTURE OF SARS-COV-2 RBD IN COMPLEX WITH NANOBODIES NB21 REMARK 900 AND NB36 DBREF 7MEJ A 1 117 PDB 7MEJ 7MEJ 1 117 DBREF 7MEJ R 333 526 UNP P0DTC2 SPIKE_SARS2 333 526 DBREF 7MEJ B 2 112 PDB 7MEJ 7MEJ 2 112 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 R 194 THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA THR SEQRES 2 R 194 ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG ILE SEQRES 3 R 194 SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SER SEQRES 4 R 194 ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER PRO SEQRES 5 R 194 THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR ALA SEQRES 6 R 194 ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN ILE SEQRES 7 R 194 ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN TYR SEQRES 8 R 194 LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA TRP SEQRES 9 R 194 ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN TYR SEQRES 10 R 194 ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU LYS SEQRES 11 R 194 PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN ALA SEQRES 12 R 194 GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN CYS SEQRES 13 R 194 TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR ASN SEQRES 14 R 194 GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SER SEQRES 15 R 194 PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 1 B 123 VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN ALA SEQRES 2 B 123 GLY GLY SER LEU THR LEU THR CYS ALA ALA SER GLY ARG SEQRES 3 B 123 THR PHE SER SER GLU THR MET ASP MET GLY TRP PHE ARG SEQRES 4 B 123 GLN ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA ALA ASP SEQRES 5 B 123 SER TRP ASN ASP GLY SER THR TYR TYR ALA ASP SER VAL SEQRES 6 B 123 LYS GLY ARG PHE THR ILE SER ARG ASP SER ALA LYS ASN SEQRES 7 B 123 THR LEU TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP SEQRES 8 B 123 THR ALA VAL TYR TYR CYS ALA ALA GLU THR TYR SER ILE SEQRES 9 B 123 TYR GLU LYS ASP ASP SER TRP GLY TYR TRP GLY GLN GLY SEQRES 10 B 123 THR GLN VAL THR VAL SER HELIX 1 AA1 CYS R 336 VAL R 341 5 6 HELIX 2 AA2 SER R 366 SER R 371 1 6 HELIX 3 AA3 ARG R 403 ILE R 410 5 8 HELIX 4 AA4 LEU B 11 GLY B 15 5 5 HELIX 5 AA5 SER B 73 THR B 77 5 5 SHEET 1 AA1 2 LEU A 4 VAL A 5 0 SHEET 2 AA1 2 ALA A 23 VAL A 24 -1 O ALA A 23 N VAL A 5 SHEET 1 AA2 3 GLU A 44 ILE A 49 0 SHEET 2 AA2 3 VAL A 32 ARG A 36 -1 N ARG A 36 O GLU A 44 SHEET 3 AA2 3 TYR A 92 ALA A 95 -1 O ALA A 95 N GLY A 33 SHEET 1 AA3 4 THR R 376 TYR R 380 0 SHEET 2 AA3 4 GLY R 431 ASN R 437 -1 O VAL R 433 N LYS R 378 SHEET 3 AA3 4 TYR R 508 GLU R 516 -1 O LEU R 513 N CYS R 432 SHEET 4 AA3 4 ASN R 394 ILE R 402 -1 N ASN R 394 O GLU R 516 SHEET 1 AA4 2 LEU R 452 TYR R 453 0 SHEET 2 AA4 2 GLN R 493 SER R 494 -1 O GLN R 493 N TYR R 453 SHEET 1 AA5 2 VAL B 5 GLU B 6 0 SHEET 2 AA5 2 GLN B 108 VAL B 109 1 O GLN B 108 N GLU B 6 SSBOND 1 CYS A 22 CYS A 94 1555 1555 2.04 SSBOND 2 CYS R 336 CYS R 361 1555 1555 2.03 SSBOND 3 CYS R 379 CYS R 432 1555 1555 2.04 SSBOND 4 CYS R 391 CYS R 525 1555 1555 2.03 SSBOND 5 CYS R 480 CYS R 488 1555 1555 2.03 SSBOND 6 CYS B 22 CYS B 92 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