HEADER DNA BINDING PROTEIN/DNA 21-SEP-20 7D3X TITLE NON-SPECIFIC AND SPECIFIC INTERACTIONS WORK COOPERATIVELY TO PROMOTE TITLE 2 CYTIDINE DEAMINATION CATALYZED BY APOBEC3A COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA DC->DU-EDITING ENZYME APOBEC-3A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: A3A,PHORBOLIN-1; COMPND 5 EC: 3.5.4.38; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*AP*TP*TP*TP*TP*CP*AP*AP*TP*T)-3'); COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: APOBEC3A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.CAO,Y.LIU REVDAT 4 15-MAY-24 7D3X 1 REMARK REVDAT 3 14-JUN-23 7D3X 1 REMARK REVDAT 2 20-APR-22 7D3X 1 AUTHOR JRNL REVDAT 1 06-OCT-21 7D3X 0 JRNL AUTH Y.LIU,W.LAN,C.WANG,C.CAO JRNL TITL TWO DIFFERENT KINDS OF INTERACTION MODES OF DEAMINASE JRNL TITL 2 APOBEC3A WITH SINGLE-STRANDED DNA IN SOLUTION DETECTED BY JRNL TITL 3 NUCLEAR MAGNETIC RESONANCE. JRNL REF PROTEIN SCI. V. 31 443 2022 JRNL REFN ESSN 1469-896X JRNL PMID 34792260 JRNL DOI 10.1002/PRO.4242 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7D3X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300018600. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.3 REMARK 210 IONIC STRENGTH : 375 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 25 MM SODIUM PHOSPHATE, 200 MM REMARK 210 SODIUM CHLORIDE, 50 UM ZINC REMARK 210 CHLORIDE, 5 MM DTT, 0.28 MM [U- REMARK 210 13C; U-15N] A3A, 0.56 MM DNA, 90% REMARK 210 H2O/10% D2O; 25 MM SODIUM REMARK 210 PHOSPHATE, 200 MM SODIUM REMARK 210 CHLORIDE, 50 UM ZINC CHLORIDE, 5 REMARK 210 MM DTT, 0.28 MM [U-13C; U-15N] REMARK 210 A3A, 0.56 MM DNA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HN(CO)CA; 3D HCCH- REMARK 210 TOCSY; 2D 1H-13C HSQC; 2D 1H-15N REMARK 210 HSQC; 3D 1H-15N TOCSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 3D 1H-13C NOESY AROMATIC; 2D REMARK 210 FILTER TOCSY; 2D FILTER NOESY; REMARK 210 3D 15N-FILTER-EDIT NOESY; 3D 13C- REMARK 210 FILTER-EDIT NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DD2 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; AGILENT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRDRAW, SPARKY, X-PLOR NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : 20 REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 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 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 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 OG1 THR A 31 HE1 TRP A 98 1.54 REMARK 500 H ASP A 41 O THR A 44 1.59 REMARK 500 OD1 ASP A 180 H GLU A 181 1.59 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 DT B 203 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT B 209 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DT B 203 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 3 DT B 201 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 3 DT B 203 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 3 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 3 DT B 209 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 4 DT B 203 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 4 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 4 DT B 209 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 5 DT B 201 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 5 DT B 203 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 5 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 5 DT B 209 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 6 DT B 203 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 6 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 7 DT B 203 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 7 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 8 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 9 DT B 203 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 9 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 9 DT B 209 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 10 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 10 DT B 209 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 11 DT B 209 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 12 DT B 203 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 12 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 13 DT B 201 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 13 DT B 203 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 13 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 13 DT B 209 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 14 DT B 203 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 14 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 14 DT B 209 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 15 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 16 DT B 203 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 16 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 17 DT B 201 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 17 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 18 DT B 201 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 18 DT B 203 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 18 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 18 DT B 209 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 19 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 20 DT B 203 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 20 DT B 208 C6 - C5 - C7 ANGL. DEV. = -3.6 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 1 ASN A 23 3.27 -57.24 REMARK 500 1 ARG A 28 102.93 -167.72 REMARK 500 1 ASN A 61 81.60 157.78 REMARK 500 1 ARG A 69 -60.69 -132.52 REMARK 500 1 SER A 103 38.71 -85.08 REMARK 500 1 ASN A 117 71.59 -118.05 REMARK 500 1 TYR A 130 68.80 -106.42 REMARK 500 1 ASP A 131 -118.98 -92.31 REMARK 500 1 TYR A 132 -162.79 159.16 REMARK 500 1 ASP A 133 169.06 -40.72 REMARK 500 1 ALA A 148 32.14 -66.85 REMARK 500 2 ASN A 23 2.28 -56.26 REMARK 500 2 ARG A 28 99.81 -168.76 REMARK 500 2 ASN A 61 79.56 157.27 REMARK 500 2 ARG A 69 -65.85 -125.45 REMARK 500 2 SER A 103 140.90 153.48 REMARK 500 2 TYR A 130 76.19 -105.14 REMARK 500 2 ASP A 131 -117.45 -98.29 REMARK 500 2 TYR A 132 -163.43 158.35 REMARK 500 2 ASP A 133 176.20 -42.45 REMARK 500 2 LEU A 135 -9.93 -53.00 REMARK 500 2 ALA A 148 31.48 -66.17 REMARK 500 2 ASP A 167 69.69 -113.44 REMARK 500 3 HIS A 11 4.18 -62.70 REMARK 500 3 ARG A 28 100.80 -171.17 REMARK 500 3 ASN A 61 77.72 158.91 REMARK 500 3 SER A 103 55.65 -94.63 REMARK 500 3 TYR A 130 71.11 -106.06 REMARK 500 3 ASP A 131 -118.64 -94.08 REMARK 500 3 TYR A 132 -162.84 158.14 REMARK 500 3 ASP A 133 175.11 -42.41 REMARK 500 3 ALA A 148 32.28 -67.71 REMARK 500 4 ARG A 10 18.04 -66.73 REMARK 500 4 HIS A 11 35.30 -69.59 REMARK 500 4 ASP A 14 108.30 -47.79 REMARK 500 4 ASN A 23 2.86 -56.83 REMARK 500 4 ARG A 28 94.50 -161.79 REMARK 500 4 GLN A 50 -84.56 -152.30 REMARK 500 4 HIS A 51 -0.92 57.79 REMARK 500 4 ASN A 61 92.39 159.12 REMARK 500 4 TYR A 130 69.53 -106.32 REMARK 500 4 ASP A 131 -118.90 -93.05 REMARK 500 4 TYR A 132 -162.38 159.13 REMARK 500 4 ASP A 133 174.35 -42.17 REMARK 500 4 ALA A 148 32.14 -66.90 REMARK 500 4 MET A 153 170.52 -58.50 REMARK 500 5 ARG A 10 23.00 -73.34 REMARK 500 5 ASN A 23 2.15 -58.74 REMARK 500 5 MET A 48 -163.12 -70.66 REMARK 500 5 GLN A 50 89.08 -176.29 REMARK 500 REMARK 500 THIS ENTRY HAS 244 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 70 ND1 REMARK 620 2 CYS A 101 SG 107.6 REMARK 620 3 CYS A 106 SG 112.6 103.8 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36389 RELATED DB: BMRB REMARK 900 NON-SPECIFIC AND SPECIFIC INTERACTIONS WORK COOPERATIVELY TO REMARK 900 PROMOTE CYTIDINE DEAMINATION CATALYZED BY APOBEC3A DBREF 7D3X A 1 199 UNP P31941 ABC3A_HUMAN 1 199 DBREF 7D3X B 200 209 PDB 7D3X 7D3X 200 209 SEQADV 7D3X ASN A 63 UNP P31941 LEU 63 ENGINEERED MUTATION SEQADV 7D3X SER A 64 UNP P31941 CYS 64 ENGINEERED MUTATION SEQADV 7D3X GLN A 72 UNP P31941 GLU 72 ENGINEERED MUTATION SEQADV 7D3X GLN A 171 UNP P31941 CYS 171 ENGINEERED MUTATION SEQRES 1 A 199 MET GLU ALA SER PRO ALA SER GLY PRO ARG HIS LEU MET SEQRES 2 A 199 ASP PRO HIS ILE PHE THR SER ASN PHE ASN ASN GLY ILE SEQRES 3 A 199 GLY ARG HIS LYS THR TYR LEU CYS TYR GLU VAL GLU ARG SEQRES 4 A 199 LEU ASP ASN GLY THR SER VAL LYS MET ASP GLN HIS ARG SEQRES 5 A 199 GLY PHE LEU HIS ASN GLN ALA LYS ASN LEU ASN SER GLY SEQRES 6 A 199 PHE TYR GLY ARG HIS ALA GLN LEU ARG PHE LEU ASP LEU SEQRES 7 A 199 VAL PRO SER LEU GLN LEU ASP PRO ALA GLN ILE TYR ARG SEQRES 8 A 199 VAL THR TRP PHE ILE SER TRP SER PRO CYS PHE SER TRP SEQRES 9 A 199 GLY CYS ALA GLY GLU VAL ARG ALA PHE LEU GLN GLU ASN SEQRES 10 A 199 THR HIS VAL ARG LEU ARG ILE PHE ALA ALA ARG ILE TYR SEQRES 11 A 199 ASP TYR ASP PRO LEU TYR LYS GLU ALA LEU GLN MET LEU SEQRES 12 A 199 ARG ASP ALA GLY ALA GLN VAL SER ILE MET THR TYR ASP SEQRES 13 A 199 GLU PHE LYS HIS CYS TRP ASP THR PHE VAL ASP HIS GLN SEQRES 14 A 199 GLY GLN PRO PHE GLN PRO TRP ASP GLY LEU ASP GLU HIS SEQRES 15 A 199 SER GLN ALA LEU SER GLY ARG LEU ARG ALA ILE LEU GLN SEQRES 16 A 199 ASN GLN GLY ASN SEQRES 1 B 10 DA DT DT DT DT DC DA DA DT DT HET ZN A 201 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ HELIX 1 AA1 ASP A 14 PHE A 22 1 9 HELIX 2 AA2 HIS A 70 GLN A 83 1 14 HELIX 3 AA3 GLY A 105 ASN A 117 1 13 HELIX 4 AA4 LEU A 135 GLY A 147 1 13 HELIX 5 AA5 THR A 154 VAL A 166 1 13 HELIX 6 AA6 GLY A 178 ASN A 199 1 22 SHEET 1 AA1 3 THR A 44 LYS A 47 0 SHEET 2 AA1 3 TYR A 32 ASP A 41 -1 N ASP A 41 O THR A 44 SHEET 3 AA1 3 GLY A 53 HIS A 56 -1 O LEU A 55 N LEU A 33 SHEET 1 AA2 5 THR A 44 LYS A 47 0 SHEET 2 AA2 5 TYR A 32 ASP A 41 -1 N ASP A 41 O THR A 44 SHEET 3 AA2 5 TYR A 90 TRP A 98 -1 O PHE A 95 N CYS A 34 SHEET 4 AA2 5 ARG A 121 ARG A 128 1 O ARG A 123 N TRP A 94 SHEET 5 AA2 5 VAL A 150 ILE A 152 1 O SER A 151 N ALA A 126 LINK ND1 HIS A 70 ZN ZN A 201 1555 1555 2.00 LINK SG CYS A 101 ZN ZN A 201 1555 1555 2.29 LINK SG CYS A 106 ZN ZN A 201 1555 1555 2.29 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