HEADER VIRAL PROTEIN 02-SEP-23 8U1T TITLE SARS-COV-2 ENVELOPE PROTEIN TRANSMEMBRANE DOMAIN: DIMERIC STRUCTURE TITLE 2 DETERMINED BY SOLID-STATE NMR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE SMALL MEMBRANE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: E,SM PROTEIN; 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 GENE: E, 4; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SARS-COV-2, ENVELOPE PROTEIN, E PROTEIN, TRANSMEMBRANE DOMAIN, KEYWDS 2 MEMBRANE PROTEIN, PISEMA, PISA WHEEL, DARR, VIRAL PROTEIN EXPDTA SOLID-STATE NMR NUMMDL 14 AUTHOR R.ZHANG,H.QIN,R.PRASAD,R.FU,H.X.ZHOU,T.CROSS REVDAT 2 15-MAY-24 8U1T 1 REMARK REVDAT 1 15-NOV-23 8U1T 0 JRNL AUTH R.ZHANG,H.QIN,R.PRASAD,R.FU,H.X.ZHOU,T.A.CROSS JRNL TITL DIMERIC TRANSMEMBRANE STRUCTURE OF THE SARS-COV-2 E PROTEIN. JRNL REF COMMUN BIOL V. 6 1109 2023 JRNL REFN ESSN 2399-3642 JRNL PMID 37914906 JRNL DOI 10.1038/S42003-023-05490-X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.ZHANG,H.QIN,R.PRASAD,R.FU,H.X.ZHOU,T.A.CROSS REMARK 1 TITL DIMERIC TRANSMEMBRANE STRUCTURE OF THE SARS-COV-2 E PROTEIN. REMARK 1 REF BIORXIV 2023 REMARK 1 REFN ISSN 2692-8205 REMARK 1 PMID 37214926 REMARK 1 DOI 10.1101/2023.05.07.539752 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NAMD REMARK 3 AUTHORS : UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN: REMARK 3 THEORETICAL AND COMPUTATIONAL BIOPHYSICS GROUP REMARK 3 (TCB), PARALLEL PROGRAMMING LABORATORY (PPL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8U1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1000277080. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295; 295 REMARK 210 PH : 7.5; 7.5 REMARK 210 IONIC STRENGTH : 5; 5 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 80 UG/ML [U-100% 15N] SARS-COV-2 REMARK 210 ENVELOPE PROTEIN TRANSMEMBRANE REMARK 210 PEPTIDE, 400 UG/ML POPC, 100 UG/ REMARK 210 ML POPG, AQUEOUS BUFFER; 80 UG/ REMARK 210 ML [U-15N]-ILE SARS-COV-2 REMARK 210 ENVELOPE PROTEIN TRANSMEMBRANE REMARK 210 PEPTIDE, 400 UG/ML POPC, 100 UG/ REMARK 210 ML POPG, AQUEOUS BUFFER; 80 UG/ REMARK 210 ML [U-15N]-PHE SARS-COV-2 REMARK 210 ENVELOPE PROTEIN TRANSMEMBRANE REMARK 210 PEPTIDE, 400 UG/ML POPC, 100 UG/ REMARK 210 ML POPG, AQUEOUS BUFFER; 80 UG/ REMARK 210 ML [U-15N]-ALA SARS-COV-2 REMARK 210 ENVELOPE PROTEIN TRANSMEMBRANE REMARK 210 PEPTIDE, 400 UG/ML POPC, 100 UG/ REMARK 210 ML POPG, AQUEOUS BUFFER; 80 UG/ REMARK 210 ML [U-15N]-VAL SARS-COV-2 REMARK 210 ENVELOPE PROTEIN TRANSMEMBRANE REMARK 210 PEPTIDE, 400 UG/ML POPC, 100 UG/ REMARK 210 ML POPG, AQUEOUS BUFFER; 80 UG/ REMARK 210 ML [U-15N]-THR SARS-COV-2 REMARK 210 ENVELOPE PROTEIN TRANSMEMBRANE REMARK 210 PEPTIDE, 400 UG/ML POPC, 100 UG/ REMARK 210 ML POPG, AQUEOUS BUFFER; 80 UG/ REMARK 210 ML [U-15N]-LEU SARS-COV-2 REMARK 210 ENVELOPE PROTEIN TRANSMEMBRANE REMARK 210 PEPTIDE, 400 UG/ML POPC, 100 UG/ REMARK 210 ML POPG, AQUEOUS BUFFER; 40 UG/ REMARK 210 ML [U-13C]-LEU, [U-13C]-VAL SARS- REMARK 210 COV-2 ENVELOPE PROTEIN REMARK 210 TRANSMEMBRANE PEPTIDE, 400 UG/ML REMARK 210 POPC, 100 UG/ML POPG, AQUEOUS REMARK 210 BUFFER; 20 UG/ML [U-13C]-LEU, [U- REMARK 210 13C]-PHE SARS-COV-2 ENVELOPE REMARK 210 PROTEIN TRANSMEMBRANE PEPTIDE, REMARK 210 400 UG/ML POPC, 100 UG/ML POPG, REMARK 210 AQUEOUS BUFFER; 20 UG/ML [U-13C]- REMARK 210 VAL, [U-13C]-MET SARS-COV-2 REMARK 210 ENVELOPE PROTEIN TRANSMEMBRANE REMARK 210 PEPTIDE, 400 UG/ML POPC, 100 UG/ REMARK 210 ML POPG, AQUEOUS BUFFER; 100 REMARK 210 SATURATED [U-15N] AMMONIUM REMARK 210 CHLORIDE SALT, AQUEOUS BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N PISEMA; 2D 1H-13C REMARK 210 DARR; 1D ZG REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, X-PLOR NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 14 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 217 REMARK 217 SOLID STATE NMR STUDY REMARK 217 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLID REMARK 217 STATE NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 217 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 217 THESE RECORDS ARE MEANINGLESS. 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 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-14 REMARK 465 RES C SSSEQI REMARK 465 SER A 9 REMARK 465 ASN A 10 REMARK 465 ALA A 11 REMARK 465 SER B 9 REMARK 465 ASN B 10 REMARK 465 ALA B 11 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 2 LEU B 27 CA LEU B 27 CB 0.157 REMARK 500 5 SER A 16 CA SER A 16 CB 0.103 REMARK 500 5 VAL B 17 CB VAL B 17 CG2 0.132 REMARK 500 5 PHE B 23 CB PHE B 23 CG -0.107 REMARK 500 10 SER A 16 CA SER A 16 CB 0.120 REMARK 500 10 PHE A 23 CB PHE A 23 CG 0.103 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 1 VAL A 14 CA - CB - CG1 ANGL. DEV. = 11.5 DEGREES REMARK 500 1 PHE A 23 CB - CG - CD1 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 VAL A 29 CG1 - CB - CG2 ANGL. DEV. = -10.8 DEGREES REMARK 500 1 PHE B 23 CB - CG - CD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 2 PHE B 20 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 PHE B 20 CG - CD1 - CE1 ANGL. DEV. = -6.8 DEGREES REMARK 500 2 PHE B 23 CB - CG - CD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 2 PHE B 23 CB - CG - CD1 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 PHE B 26 CB - CG - CD2 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 PHE A 20 CB - CG - CD2 ANGL. DEV. = 7.3 DEGREES REMARK 500 3 PHE A 20 CB - CG - CD1 ANGL. DEV. = -6.7 DEGREES REMARK 500 3 PHE A 23 CB - CG - CD1 ANGL. DEV. = -4.2 DEGREES REMARK 500 3 PHE B 26 CB - CG - CD2 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 PHE B 23 CB - CG - CD1 ANGL. DEV. = -5.1 DEGREES REMARK 500 5 THR A 30 N - CA - CB ANGL. DEV. = 11.9 DEGREES REMARK 500 5 PHE B 26 CB - CG - CD2 ANGL. DEV. = 9.5 DEGREES REMARK 500 6 PHE B 20 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 6 PHE B 23 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 7 VAL A 14 CA - CB - CG2 ANGL. DEV. = -10.3 DEGREES REMARK 500 7 PHE B 20 CB - CG - CD2 ANGL. DEV. = 4.4 DEGREES REMARK 500 7 VAL B 25 CA - CB - CG2 ANGL. DEV. = -9.8 DEGREES REMARK 500 8 LEU A 21 CB - CG - CD2 ANGL. DEV. = 10.5 DEGREES REMARK 500 8 VAL B 17 CA - CB - CG2 ANGL. DEV. = -11.1 DEGREES REMARK 500 8 PHE B 26 CB - CG - CD2 ANGL. DEV. = -7.5 DEGREES REMARK 500 9 PHE A 20 CB - CG - CD2 ANGL. DEV. = 5.1 DEGREES REMARK 500 9 PHE A 20 CB - CG - CD1 ANGL. DEV. = -7.1 DEGREES REMARK 500 9 ALA A 36 N - CA - CB ANGL. DEV. = -9.8 DEGREES REMARK 500 10 PHE B 23 CB - CG - CD2 ANGL. DEV. = 5.1 DEGREES REMARK 500 10 PHE B 23 CB - CG - CD1 ANGL. DEV. = -5.0 DEGREES REMARK 500 10 PHE B 26 CB - CG - CD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 10 LEU B 27 O - C - N ANGL. DEV. = -9.9 DEGREES REMARK 500 11 PHE B 20 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 11 PHE B 23 CB - CG - CD1 ANGL. DEV. = -6.7 DEGREES REMARK 500 11 VAL B 29 CA - CB - CG1 ANGL. DEV. = 9.7 DEGREES REMARK 500 12 PHE A 20 CB - CG - CD1 ANGL. DEV. = -5.1 DEGREES REMARK 500 12 PHE A 26 CB - CG - CD1 ANGL. DEV. = -6.0 DEGREES REMARK 500 12 PHE B 20 CG - CD2 - CE2 ANGL. DEV. = -7.6 DEGREES REMARK 500 13 LEU A 19 CB - CG - CD1 ANGL. DEV. = 10.5 DEGREES REMARK 500 13 PHE A 26 CB - CG - CD1 ANGL. DEV. = -6.5 DEGREES REMARK 500 13 PHE B 26 CB - CG - CD2 ANGL. DEV. = 4.6 DEGREES REMARK 500 14 THR A 30 N - CA - CB ANGL. DEV. = 11.8 DEGREES REMARK 500 14 PHE B 26 CB - CG - CD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 14 PHE B 26 CB - CG - CD1 ANGL. DEV. = -6.3 DEGREES REMARK 500 14 ALA B 32 N - CA - CB ANGL. DEV. = -8.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 PHE A 26 0.08 SIDE CHAIN REMARK 500 3 PHE B 23 0.09 SIDE CHAIN REMARK 500 4 PHE A 20 0.07 SIDE CHAIN REMARK 500 4 PHE B 20 0.09 SIDE CHAIN REMARK 500 4 PHE B 26 0.06 SIDE CHAIN REMARK 500 6 PHE B 23 0.07 SIDE CHAIN REMARK 500 8 PHE B 26 0.07 SIDE CHAIN REMARK 500 9 PHE B 26 0.07 SIDE CHAIN REMARK 500 11 PHE A 26 0.08 SIDE CHAIN REMARK 500 12 PHE B 20 0.08 SIDE CHAIN REMARK 500 14 PHE A 20 0.10 SIDE CHAIN REMARK 500 14 PHE A 23 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31104 RELATED DB: BMRB REMARK 900 SARS-COV-2 ENVELOPE PROTEIN TRANSMEMBRANE DOMAIN: DIMERIC STRUCTURE REMARK 900 DETERMINED BY SOLID-STATE NMR DBREF 8U1T A 12 37 UNP P0DTC4 VEMP_SARS2 12 37 DBREF 8U1T B 12 37 UNP P0DTC4 VEMP_SARS2 12 37 SEQADV 8U1T SER A 9 UNP P0DTC4 EXPRESSION TAG SEQADV 8U1T ASN A 10 UNP P0DTC4 EXPRESSION TAG SEQADV 8U1T ALA A 11 UNP P0DTC4 EXPRESSION TAG SEQADV 8U1T SER B 9 UNP P0DTC4 EXPRESSION TAG SEQADV 8U1T ASN B 10 UNP P0DTC4 EXPRESSION TAG SEQADV 8U1T ALA B 11 UNP P0DTC4 EXPRESSION TAG SEQRES 1 A 29 SER ASN ALA LEU ILE VAL ASN SER VAL LEU LEU PHE LEU SEQRES 2 A 29 ALA PHE VAL VAL PHE LEU LEU VAL THR LEU ALA ILE LEU SEQRES 3 A 29 THR ALA LEU SEQRES 1 B 29 SER ASN ALA LEU ILE VAL ASN SER VAL LEU LEU PHE LEU SEQRES 2 B 29 ALA PHE VAL VAL PHE LEU LEU VAL THR LEU ALA ILE LEU SEQRES 3 B 29 THR ALA LEU HELIX 1 AA1 LEU A 12 LEU A 37 1 26 HELIX 2 AA2 ILE B 13 LEU B 37 1 25 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 MODEL 1