HEADER SIGNALING PROTEIN 13-AUG-18 6AGP TITLE STRUCTURE OF RAC1 IN THE LOW-AFFINITY STATE FOR MG2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CELL MIGRATION-INDUCING GENE 5 PROTEIN,RAS-LIKE PROTEIN COMPND 5 TC25,P21-RAC1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RAC1, TC25, MIG5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: RP+; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PGEX6P-1 KEYWDS NUCLEOTIDE BINDING, GTPASE ACTIVITY, GTP BINDING, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.TOYAMA,K.KONTANI,T.KATADA,I.SHIMADA REVDAT 3 01-MAY-24 6AGP 1 REMARK REVDAT 2 20-NOV-19 6AGP 1 JRNL REMARK REVDAT 1 20-MAR-19 6AGP 0 JRNL AUTH Y.TOYAMA,K.KONTANI,T.KATADA,I.SHIMADA JRNL TITL CONFORMATIONAL LANDSCAPE ALTERNATIONS PROMOTE ONCOGENIC JRNL TITL 2 ACTIVITIES OF RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 AS JRNL TITL 3 REVEALED BY NMR. JRNL REF SCI ADV V. 5 V8945 2019 JRNL REFN ESSN 2375-2548 JRNL PMID 30891502 JRNL DOI 10.1126/SCIADV.AAV8945 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6AGP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-AUG-18. REMARK 100 THE DEPOSITION ID IS D_1300008691. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 20 MM HEPES, 5 MM MGCL2, 0.5 MM REMARK 210 GDP, 0.1 MM DSS, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 HH12 ARG A 94 OE1 GLU A 148 1.57 REMARK 500 OD1 ASP A 65 HH22 ARG A 68 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 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 TYR A 72 CB - CG - CD2 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 TYR A 72 CB - CG - CD1 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 ARG A 102 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 ARG A 120 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 ARG A 174 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 2 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 2 TYR A 72 CB - CG - CD2 ANGL. DEV. = 5.1 DEGREES REMARK 500 2 TYR A 72 CB - CG - CD1 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 ARG A 102 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 ARG A 120 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 ARG A 174 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 3 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 3 TYR A 72 CB - CG - CD2 ANGL. DEV. = 5.1 DEGREES REMARK 500 3 TYR A 72 CB - CG - CD1 ANGL. DEV. = -5.2 DEGREES REMARK 500 3 ARG A 102 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 3 ARG A 120 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG A 174 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 4 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 4 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 4 TYR A 72 CB - CG - CD2 ANGL. DEV. = 5.1 DEGREES REMARK 500 4 TYR A 72 CB - CG - CD1 ANGL. DEV. = -5.2 DEGREES REMARK 500 4 ARG A 102 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 4 ARG A 120 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 ARG A 174 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 5 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 5 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 5 TYR A 72 CB - CG - CD2 ANGL. DEV. = 5.1 DEGREES REMARK 500 5 TYR A 72 CB - CG - CD1 ANGL. DEV. = -5.2 DEGREES REMARK 500 5 ARG A 102 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 5 ARG A 120 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 ARG A 174 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 6 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 6 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 6 TYR A 72 CB - CG - CD2 ANGL. DEV. = 5.1 DEGREES REMARK 500 6 TYR A 72 CB - CG - CD1 ANGL. DEV. = -5.2 DEGREES REMARK 500 6 ARG A 102 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 6 ARG A 120 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 ARG A 174 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 7 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 7 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 7 TYR A 72 CB - CG - CD2 ANGL. DEV. = 5.1 DEGREES REMARK 500 7 TYR A 72 CB - CG - CD1 ANGL. DEV. = -5.2 DEGREES REMARK 500 7 ARG A 102 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 7 ARG A 120 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 ARG A 174 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 8 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 140 ANGLE DEVIATIONS. 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 ASP A 11 151.52 -48.68 REMARK 500 1 ALA A 27 145.97 107.48 REMARK 500 1 CYS A 31 93.37 -23.73 REMARK 500 1 ASN A 39 163.28 152.88 REMARK 500 1 CYS A 74 30.43 73.22 REMARK 500 1 LYS A 96 -62.88 -132.81 REMARK 500 2 ASP A 11 151.52 -48.68 REMARK 500 2 ASN A 26 -140.88 -52.43 REMARK 500 2 PHE A 28 104.47 62.98 REMARK 500 2 CYS A 31 -110.40 23.01 REMARK 500 2 TYR A 32 -91.38 -148.12 REMARK 500 2 PHE A 37 58.20 -108.95 REMARK 500 2 TYR A 40 1.42 -68.61 REMARK 500 2 ALA A 42 116.36 50.55 REMARK 500 2 ASN A 43 45.44 -87.70 REMARK 500 2 VAL A 44 137.62 -36.33 REMARK 500 2 CYS A 74 30.36 73.24 REMARK 500 2 LYS A 96 -62.88 -132.81 REMARK 500 3 ASP A 11 151.52 -48.68 REMARK 500 3 PRO A 29 -161.63 -49.18 REMARK 500 3 TYR A 32 -5.19 71.63 REMARK 500 3 ASP A 47 73.91 -30.52 REMARK 500 3 CYS A 74 30.36 73.24 REMARK 500 3 LYS A 96 -62.88 -132.81 REMARK 500 4 ASP A 11 151.52 -48.68 REMARK 500 4 THR A 25 -13.67 95.28 REMARK 500 4 ASN A 26 29.82 32.07 REMARK 500 4 PHE A 28 175.46 44.78 REMARK 500 4 CYS A 31 -107.80 -76.79 REMARK 500 4 TYR A 32 155.95 167.78 REMARK 500 4 PHE A 37 -75.68 -77.04 REMARK 500 4 ASP A 38 49.18 39.97 REMARK 500 4 TYR A 40 -143.08 -54.30 REMARK 500 4 MET A 45 85.76 -157.36 REMARK 500 4 ASP A 47 18.16 55.66 REMARK 500 4 LYS A 96 -62.88 -132.81 REMARK 500 5 ASP A 11 151.52 -48.68 REMARK 500 5 ALA A 27 -103.79 27.97 REMARK 500 5 CYS A 31 98.43 49.19 REMARK 500 5 TYR A 32 -70.87 -57.33 REMARK 500 5 ASP A 38 -118.18 -6.34 REMARK 500 5 ALA A 42 160.11 85.52 REMARK 500 5 CYS A 74 30.37 73.27 REMARK 500 5 LYS A 96 -62.88 -132.81 REMARK 500 6 ASP A 11 151.52 -48.68 REMARK 500 6 THR A 25 140.59 -19.53 REMARK 500 6 PHE A 28 151.43 54.97 REMARK 500 6 TYR A 32 -112.14 -123.10 REMARK 500 6 ILE A 33 115.19 51.60 REMARK 500 6 TYR A 40 68.84 -69.27 REMARK 500 REMARK 500 THIS ENTRY HAS 203 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 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 17 OG1 REMARK 620 2 GDP A 201 O2B 82.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36206 RELATED DB: BMRB REMARK 900 STRUCTURE OF RAC1 IN THE LOW-AFFINITY STATE FOR MG2+ REMARK 900 RELATED ID: 27577 RELATED DB: BMRB REMARK 900 RESONANCE ASSIGNMENTS FOR RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE REMARK 900 1 BOUND TO GDP AND MG2+ DBREF 6AGP A 1 181 UNP P63000 RAC1_HUMAN 1 181 SEQADV 6AGP CYS A 31 UNP P63000 GLU 31 ENGINEERED MUTATION SEQADV 6AGP CYS A 63 UNP P63000 ASP 63 ENGINEERED MUTATION SEQADV 6AGP CYS A 74 UNP P63000 GLN 74 ENGINEERED MUTATION SEQADV 6AGP CYS A 160 UNP P63000 LEU 160 ENGINEERED MUTATION SEQRES 1 A 181 MET GLN ALA ILE LYS CYS VAL VAL VAL GLY ASP GLY ALA SEQRES 2 A 181 VAL GLY LYS THR CYS LEU LEU ILE SER TYR THR THR ASN SEQRES 3 A 181 ALA PHE PRO GLY CYS TYR ILE PRO THR VAL PHE ASP ASN SEQRES 4 A 181 TYR SER ALA ASN VAL MET VAL ASP GLY LYS PRO VAL ASN SEQRES 5 A 181 LEU GLY LEU TRP ASP THR ALA GLY GLN GLU CYS TYR ASP SEQRES 6 A 181 ARG LEU ARG PRO LEU SER TYR PRO CYS THR ASP VAL PHE SEQRES 7 A 181 LEU ILE CYS PHE SER LEU VAL SER PRO ALA SER PHE GLU SEQRES 8 A 181 ASN VAL ARG ALA LYS TRP TYR PRO GLU VAL ARG HIS HIS SEQRES 9 A 181 CYS PRO ASN THR PRO ILE ILE LEU VAL GLY THR LYS LEU SEQRES 10 A 181 ASP LEU ARG ASP ASP LYS ASP THR ILE GLU LYS LEU LYS SEQRES 11 A 181 GLU LYS LYS LEU THR PRO ILE THR TYR PRO GLN GLY LEU SEQRES 12 A 181 ALA MET ALA LYS GLU ILE GLY ALA VAL LYS TYR LEU GLU SEQRES 13 A 181 CYS SER ALA CYS THR GLN ARG GLY LEU LYS THR VAL PHE SEQRES 14 A 181 ASP GLU ALA ILE ARG ALA VAL LEU CYS PRO PRO PRO HET GDP A 201 41 HET MG A 202 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MG MG 2+ HELIX 1 AA1 GLY A 15 THR A 25 1 11 HELIX 2 AA2 ALA A 27 CYS A 31 5 5 HELIX 3 AA3 GLN A 61 ASP A 65 5 5 HELIX 4 AA4 LEU A 67 TYR A 72 5 6 HELIX 5 AA5 SER A 86 LYS A 96 1 11 HELIX 6 AA6 LYS A 96 CYS A 105 1 10 HELIX 7 AA7 LYS A 116 ARG A 120 5 5 HELIX 8 AA8 ASP A 122 LYS A 132 1 11 HELIX 9 AA9 THR A 138 ILE A 149 1 12 HELIX 10 AB1 GLY A 164 CYS A 178 1 15 SHEET 1 AA1 6 SER A 41 VAL A 46 0 SHEET 2 AA1 6 LYS A 49 TRP A 56 -1 O VAL A 51 N VAL A 44 SHEET 3 AA1 6 GLN A 2 VAL A 9 1 N CYS A 6 O GLY A 54 SHEET 4 AA1 6 VAL A 77 SER A 83 1 O LEU A 79 N VAL A 9 SHEET 5 AA1 6 ILE A 110 THR A 115 1 O THR A 115 N PHE A 82 SHEET 6 AA1 6 LYS A 153 GLU A 156 1 O LEU A 155 N GLY A 114 LINK OG1 THR A 17 MG MG A 202 1555 1555 2.08 LINK O2B GDP A 201 MG MG A 202 1555 1555 2.26 SITE 1 AC1 14 ASP A 11 GLY A 12 ALA A 13 VAL A 14 SITE 2 AC1 14 GLY A 15 LYS A 16 THR A 17 CYS A 18 SITE 3 AC1 14 LYS A 116 ASP A 118 LEU A 119 ALA A 159 SITE 4 AC1 14 CYS A 160 MG A 202 SITE 1 AC2 2 THR A 17 GDP A 201 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