HEADER MEMBRANE PROTEIN 15-MAY-22 8CTK TITLE CRYO-EM STRUCTURE OF SARS-COV-2 M PROTEIN IN A LIPID NANODISC COMPND MOL_ID: 1; COMPND 2 MOLECULE: MEMBRANE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: M,E1 GLYCOPROTEIN,MATRIX GLYCOPROTEIN,MEMBRANE GLYCOPROTEIN; COMPND 5 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 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS SARS-COV-2, CORONAVIRUS, VIRAL PROTEIN, CAPSID PROTEIN, MEMBRANE KEYWDS 2 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR K.A.DOLAN,S.G.BROHAWN REVDAT 2 02-NOV-22 8CTK 1 JRNL REVDAT 1 22-JUN-22 8CTK 0 JRNL AUTH K.A.DOLAN,M.DUTTA,D.M.KERN,A.KOTECHA,G.A.VOTH,S.G.BROHAWN JRNL TITL STRUCTURE OF SARS-COV-2 M PROTEIN IN LIPID NANODISCS. JRNL REF ELIFE V. 11 2022 JRNL REFN ESSN 2050-084X JRNL PMID 36264056 JRNL DOI 10.7554/ELIFE.81702 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.V.AFONINE REMARK 1 TITL REAL-SPACE REFINEMENT IN PHENIX FOR CRYO-EM AND REMARK 1 TITL 2 CRYSTALLOGRAPHY REMARK 1 REF ACTA CRYSTALLOGR., SECT. D: V. 74 531 2018 REMARK 1 REF 2 BIOL. CRYSTALLOGR. REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 3.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CTFFIND, 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 : 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) : 3.520 REMARK 3 NUMBER OF PARTICLES : 64966 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 8CTK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000265428. 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 : M PROTEIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 1.30 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT FORCE 1, WAIT TIME 5S, REMARK 245 BLOT TIME 3S 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 : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 1200.00 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, 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 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 ASP A 3 REMARK 465 SER A 4 REMARK 465 ASN A 5 REMARK 465 GLY A 6 REMARK 465 THR A 7 REMARK 465 ILE A 8 REMARK 465 THR A 9 REMARK 465 VAL A 10 REMARK 465 GLU A 11 REMARK 465 GLU A 12 REMARK 465 LEU A 13 REMARK 465 LYS A 14 REMARK 465 LYS A 15 REMARK 465 LEU A 16 REMARK 465 LYS A 205 REMARK 465 LEU A 206 REMARK 465 ASN A 207 REMARK 465 THR A 208 REMARK 465 ASP A 209 REMARK 465 HIS A 210 REMARK 465 SER A 211 REMARK 465 SER A 212 REMARK 465 SER A 213 REMARK 465 SER A 214 REMARK 465 ASP A 215 REMARK 465 ASN A 216 REMARK 465 ILE A 217 REMARK 465 ALA A 218 REMARK 465 LEU A 219 REMARK 465 LEU A 220 REMARK 465 VAL A 221 REMARK 465 GLN A 222 REMARK 465 SER A 223 REMARK 465 ASN A 224 REMARK 465 SER A 225 REMARK 465 LEU A 226 REMARK 465 GLU A 227 REMARK 465 VAL A 228 REMARK 465 LEU A 229 REMARK 465 PHE A 230 REMARK 465 GLN A 231 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ASP B 3 REMARK 465 SER B 4 REMARK 465 ASN B 5 REMARK 465 GLY B 6 REMARK 465 THR B 7 REMARK 465 ILE B 8 REMARK 465 THR B 9 REMARK 465 VAL B 10 REMARK 465 GLU B 11 REMARK 465 GLU B 12 REMARK 465 LEU B 13 REMARK 465 LYS B 14 REMARK 465 LYS B 15 REMARK 465 LEU B 16 REMARK 465 LYS B 205 REMARK 465 LEU B 206 REMARK 465 ASN B 207 REMARK 465 THR B 208 REMARK 465 ASP B 209 REMARK 465 HIS B 210 REMARK 465 SER B 211 REMARK 465 SER B 212 REMARK 465 SER B 213 REMARK 465 SER B 214 REMARK 465 ASP B 215 REMARK 465 ASN B 216 REMARK 465 ILE B 217 REMARK 465 ALA B 218 REMARK 465 LEU B 219 REMARK 465 LEU B 220 REMARK 465 VAL B 221 REMARK 465 GLN B 222 REMARK 465 SER B 223 REMARK 465 ASN B 224 REMARK 465 SER B 225 REMARK 465 LEU B 226 REMARK 465 GLU B 227 REMARK 465 VAL B 228 REMARK 465 LEU B 229 REMARK 465 PHE B 230 REMARK 465 GLN B 231 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 TYR A 71 35.67 -92.86 REMARK 500 PHE A 193 117.15 -161.47 REMARK 500 TYR A 199 -61.74 -95.35 REMARK 500 TYR B 71 35.67 -92.86 REMARK 500 PHE B 193 117.15 -161.47 REMARK 500 TYR B 199 -61.74 -95.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-26993 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF SARS-COV-2 M PROTEIN IN A LIPID NANODISC DBREF 8CTK A 1 222 UNP P0DTC5 VME1_SARS2 1 222 DBREF 8CTK B 1 222 UNP P0DTC5 VME1_SARS2 1 222 SEQADV 8CTK SER A 223 UNP P0DTC5 EXPRESSION TAG SEQADV 8CTK ASN A 224 UNP P0DTC5 EXPRESSION TAG SEQADV 8CTK SER A 225 UNP P0DTC5 EXPRESSION TAG SEQADV 8CTK LEU A 226 UNP P0DTC5 EXPRESSION TAG SEQADV 8CTK GLU A 227 UNP P0DTC5 EXPRESSION TAG SEQADV 8CTK VAL A 228 UNP P0DTC5 EXPRESSION TAG SEQADV 8CTK LEU A 229 UNP P0DTC5 EXPRESSION TAG SEQADV 8CTK PHE A 230 UNP P0DTC5 EXPRESSION TAG SEQADV 8CTK GLN A 231 UNP P0DTC5 EXPRESSION TAG SEQADV 8CTK SER B 223 UNP P0DTC5 EXPRESSION TAG SEQADV 8CTK ASN B 224 UNP P0DTC5 EXPRESSION TAG SEQADV 8CTK SER B 225 UNP P0DTC5 EXPRESSION TAG SEQADV 8CTK LEU B 226 UNP P0DTC5 EXPRESSION TAG SEQADV 8CTK GLU B 227 UNP P0DTC5 EXPRESSION TAG SEQADV 8CTK VAL B 228 UNP P0DTC5 EXPRESSION TAG SEQADV 8CTK LEU B 229 UNP P0DTC5 EXPRESSION TAG SEQADV 8CTK PHE B 230 UNP P0DTC5 EXPRESSION TAG SEQADV 8CTK GLN B 231 UNP P0DTC5 EXPRESSION TAG SEQRES 1 A 231 MET ALA ASP SER ASN GLY THR ILE THR VAL GLU GLU LEU SEQRES 2 A 231 LYS LYS LEU LEU GLU GLN TRP ASN LEU VAL ILE GLY PHE SEQRES 3 A 231 LEU PHE LEU THR TRP ILE CYS LEU LEU GLN PHE ALA TYR SEQRES 4 A 231 ALA ASN ARG ASN ARG PHE LEU TYR ILE ILE LYS LEU ILE SEQRES 5 A 231 PHE LEU TRP LEU LEU TRP PRO VAL THR LEU ALA CYS PHE SEQRES 6 A 231 VAL LEU ALA ALA VAL TYR ARG ILE ASN TRP ILE THR GLY SEQRES 7 A 231 GLY ILE ALA ILE ALA MET ALA CYS LEU VAL GLY LEU MET SEQRES 8 A 231 TRP LEU SER TYR PHE ILE ALA SER PHE ARG LEU PHE ALA SEQRES 9 A 231 ARG THR ARG SER MET TRP SER PHE ASN PRO GLU THR ASN SEQRES 10 A 231 ILE LEU LEU ASN VAL PRO LEU HIS GLY THR ILE LEU THR SEQRES 11 A 231 ARG PRO LEU LEU GLU SER GLU LEU VAL ILE GLY ALA VAL SEQRES 12 A 231 ILE LEU ARG GLY HIS LEU ARG ILE ALA GLY HIS HIS LEU SEQRES 13 A 231 GLY ARG CYS ASP ILE LYS ASP LEU PRO LYS GLU ILE THR SEQRES 14 A 231 VAL ALA THR SER ARG THR LEU SER TYR TYR LYS LEU GLY SEQRES 15 A 231 ALA SER GLN ARG VAL ALA GLY ASP SER GLY PHE ALA ALA SEQRES 16 A 231 TYR SER ARG TYR ARG ILE GLY ASN TYR LYS LEU ASN THR SEQRES 17 A 231 ASP HIS SER SER SER SER ASP ASN ILE ALA LEU LEU VAL SEQRES 18 A 231 GLN SER ASN SER LEU GLU VAL LEU PHE GLN SEQRES 1 B 231 MET ALA ASP SER ASN GLY THR ILE THR VAL GLU GLU LEU SEQRES 2 B 231 LYS LYS LEU LEU GLU GLN TRP ASN LEU VAL ILE GLY PHE SEQRES 3 B 231 LEU PHE LEU THR TRP ILE CYS LEU LEU GLN PHE ALA TYR SEQRES 4 B 231 ALA ASN ARG ASN ARG PHE LEU TYR ILE ILE LYS LEU ILE SEQRES 5 B 231 PHE LEU TRP LEU LEU TRP PRO VAL THR LEU ALA CYS PHE SEQRES 6 B 231 VAL LEU ALA ALA VAL TYR ARG ILE ASN TRP ILE THR GLY SEQRES 7 B 231 GLY ILE ALA ILE ALA MET ALA CYS LEU VAL GLY LEU MET SEQRES 8 B 231 TRP LEU SER TYR PHE ILE ALA SER PHE ARG LEU PHE ALA SEQRES 9 B 231 ARG THR ARG SER MET TRP SER PHE ASN PRO GLU THR ASN SEQRES 10 B 231 ILE LEU LEU ASN VAL PRO LEU HIS GLY THR ILE LEU THR SEQRES 11 B 231 ARG PRO LEU LEU GLU SER GLU LEU VAL ILE GLY ALA VAL SEQRES 12 B 231 ILE LEU ARG GLY HIS LEU ARG ILE ALA GLY HIS HIS LEU SEQRES 13 B 231 GLY ARG CYS ASP ILE LYS ASP LEU PRO LYS GLU ILE THR SEQRES 14 B 231 VAL ALA THR SER ARG THR LEU SER TYR TYR LYS LEU GLY SEQRES 15 B 231 ALA SER GLN ARG VAL ALA GLY ASP SER GLY PHE ALA ALA SEQRES 16 B 231 TYR SER ARG TYR ARG ILE GLY ASN TYR LYS LEU ASN THR SEQRES 17 B 231 ASP HIS SER SER SER SER ASP ASN ILE ALA LEU LEU VAL SEQRES 18 B 231 GLN SER ASN SER LEU GLU VAL LEU PHE GLN HELIX 1 AA1 LEU A 17 ALA A 38 1 22 HELIX 2 AA2 ASN A 43 LEU A 56 1 14 HELIX 3 AA3 LEU A 56 TYR A 71 1 16 HELIX 4 AA4 ASN A 74 ARG A 107 1 34 HELIX 5 AA5 SER A 108 ASN A 113 5 6 HELIX 6 AA6 GLU B 18 ALA B 38 1 21 HELIX 7 AA7 ASN B 43 LEU B 56 1 14 HELIX 8 AA8 LEU B 56 TYR B 71 1 16 HELIX 9 AA9 ASN B 74 ARG B 107 1 34 HELIX 10 AB1 SER B 108 ASN B 113 5 6 SHEET 1 AA1 8 ILE A 128 PRO A 132 0 SHEET 2 AA1 8 LEU A 119 PRO A 123 -1 N VAL A 122 O LEU A 129 SHEET 3 AA1 8 GLU A 167 THR A 172 -1 O THR A 169 N ASN A 121 SHEET 4 AA1 8 THR A 175 SER A 184 -1 O TYR A 179 N ILE A 168 SHEET 5 AA1 8 PHE A 193 GLY A 202 -1 O TYR A 199 N TYR A 178 SHEET 6 AA1 8 VAL A 139 LEU A 145 -1 N ALA A 142 O ALA A 194 SHEET 7 AA1 8 HIS A 148 ILE A 151 -1 O HIS A 148 N LEU A 145 SHEET 8 AA1 8 HIS A 154 ARG A 158 -1 O HIS A 154 N ILE A 151 SHEET 1 AA2 8 ILE B 128 PRO B 132 0 SHEET 2 AA2 8 LEU B 119 PRO B 123 -1 N VAL B 122 O LEU B 129 SHEET 3 AA2 8 GLU B 167 THR B 172 -1 O THR B 169 N ASN B 121 SHEET 4 AA2 8 THR B 175 SER B 184 -1 O TYR B 179 N ILE B 168 SHEET 5 AA2 8 PHE B 193 GLY B 202 -1 O TYR B 199 N TYR B 178 SHEET 6 AA2 8 VAL B 139 LEU B 145 -1 N ALA B 142 O ALA B 194 SHEET 7 AA2 8 HIS B 148 ILE B 151 -1 O HIS B 148 N LEU B 145 SHEET 8 AA2 8 HIS B 154 ARG B 158 -1 O HIS B 154 N ILE B 151 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 MTRIX1 1 -0.999992 -0.002086 0.003393 209.13262 1 MTRIX2 1 0.002070 -0.999987 -0.004567 209.67053 1 MTRIX3 1 0.003402 -0.004560 0.999984 0.05520 1