HEADER SIGNALING PROTEIN 25-AUG-22 8AU4 TITLE STRUCTURAL INSIGHTS REVEAL A HETEROTETRAMER BETWEEN ONCOGENIC K- TITLE 2 RAS4BG12V AND RGL2, A RALA/B ACTIVATOR CAVEAT 8AU4 ARG A 735 HAS WRONG CHIRALITY AT ATOM CA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAL GUANINE NUCLEOTIDE DISSOCIATION STIMULATOR-LIKE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RALGDS-LIKE 2,RALGDS-LIKE FACTOR,RAS-ASSOCIATED PROTEIN COMPND 5 RAB2L; COMPND 6 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: RGL2, RAB2L; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SMALL GTPASE RAS SIGNALLING PROTEIN-PROTEIN INTERACTION NMR X-RAY KEYWDS 2 CRYSTALLOGRAPHY, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.TARIQ,T.IKEYA,N.TOGASHI,L.FAIRALL,C.B.ALEJO,S.KAMEI,B.R.ALONSO, AUTHOR 2 M.A.M.CAMPILLO,A.HUDSON,Y.ITO,J.SCHWABE,C.DOMINGUEZ,K.TANAKA REVDAT 2 25-OCT-23 8AU4 1 JRNL REVDAT 1 23-AUG-23 8AU4 0 JRNL AUTH M.TARIQ,T.IKEYA,N.TOGASHI,L.FAIRALL,S.KAMEI, JRNL AUTH 2 S.MAYOORAMURUGAN,L.R.ABBOTT,A.HASAN,C.BUENO-ALEJO, JRNL AUTH 3 S.SUKEGAWA,B.ROMARTINEZ-ALONSO,M.A.MURO CAMPILLO,A.J.HUDSON, JRNL AUTH 4 Y.ITO,J.W.SCHWABE,C.DOMINGUEZ,K.TANAKA JRNL TITL STRUCTURAL INSIGHTS INTO THE COMPLEX OF ONCOGENIC KRAS4B JRNL TITL 2 G12V AND RGL2, A RALA/B ACTIVATOR. JRNL REF LIFE SCI ALLIANCE V. 7 2024 JRNL REFN ESSN 2575-1077 JRNL PMID 37833074 JRNL DOI 10.26508/LSA.202302080 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.TARIQ,T.IKEYA,N.TOGASHI,L.FAIRALL,C.BUENO-ALEJO,S.KAMEI, REMARK 1 AUTH 2 B.ROMARTINEZ-ALONSO,M.A.M.CAMPILLO,A.J.HUDSON,Y.ITO, REMARK 1 AUTH 3 J.W.R.SCHWABE,C.DOMINGUEZ,K.TANAKA REMARK 1 TITL STRUCTURAL INSIGHTS INTO THE COMPLEX OF ONCOGENIC REMARK 1 TITL 2 K-RAS4BG12V AND RGL2, A RALA/B ACTIVATOR REMARK 1 REF BIORXIV 2023 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2022.10.10.511529 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPALP 1.4 REMARK 3 AUTHORS : LUGINBUHL, GUNTERT, BILLETER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8AU4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1292124931. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 15N] RGL2, 90% REMARK 210 H2O/10% D2O; 1 MM [U-100% 13C; U- REMARK 210 100% 15N] RGL2, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 2D 1H-13C HSQC; 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D HNCA; 3D HN(CO)CA; REMARK 210 3D CBCA(CO)NH; 3D CBCANH; 3D REMARK 210 HBHA(CO)NH; 3D C(CO)NH; 3D H(CCO) REMARK 210 NH; 3D HCCH-COSY; 3D HCCH-TOCSY; REMARK 210 2D (HB)CB(CGCD)HD; 2D (HB) REMARK 210 CB(CGCDCE)HE; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.99.0, TOPSPIN 3.6.2, REMARK 210 AZARA 2.8.1, CCPNMR ANALYSIS REMARK 210 2.5.0 REMARK 210 METHOD USED : ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 OD2 ASP A 674 HG SER A 678 1.57 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 ASP A 690 C - N - CA ANGL. DEV. = 17.8 DEGREES REMARK 500 1 SER A 691 N - CA - CB ANGL. DEV. = -9.5 DEGREES REMARK 500 1 SER A 691 CA - C - N ANGL. DEV. = -18.8 DEGREES REMARK 500 1 ALA A 692 C - N - CA ANGL. DEV. = 24.2 DEGREES REMARK 500 1 ALA A 692 N - CA - CB ANGL. DEV. = -9.1 DEGREES REMARK 500 1 SER A 737 C - N - CA ANGL. DEV. = 17.9 DEGREES REMARK 500 2 ALA A 646 C - N - CA ANGL. DEV. = 16.9 DEGREES REMARK 500 2 ASP A 648 C - N - CA ANGL. DEV. = 28.9 DEGREES REMARK 500 3 ALA A 646 C - N - CA ANGL. DEV. = 16.3 DEGREES REMARK 500 3 ASP A 648 C - N - CA ANGL. DEV. = 25.8 DEGREES REMARK 500 5 TYR A 665 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES REMARK 500 6 ASP A 648 C - N - CA ANGL. DEV. = 25.5 DEGREES REMARK 500 7 SER A 736 C - N - CA ANGL. DEV. = 19.5 DEGREES REMARK 500 10 TYR A 665 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES REMARK 500 10 ASP A 674 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 10 ASP A 674 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 14 SER A 736 C - N - CA ANGL. DEV. = 21.1 DEGREES REMARK 500 17 ARG A 735 C - N - CA ANGL. DEV. = 19.4 DEGREES REMARK 500 17 SER A 737 N - CA - C ANGL. DEV. = 16.4 DEGREES REMARK 500 17 SER A 737 CA - C - N ANGL. DEV. = -15.0 DEGREES REMARK 500 17 THR A 738 C - N - CA ANGL. DEV. = 29.0 DEGREES REMARK 500 18 ALA A 646 C - N - CA ANGL. DEV. = 17.7 DEGREES REMARK 500 19 TYR A 665 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 19 ASP A 690 C - N - CA ANGL. DEV. = 20.4 DEGREES REMARK 500 19 SER A 691 CA - C - N ANGL. DEV. = -20.1 DEGREES REMARK 500 19 ALA A 692 C - N - CA ANGL. DEV. = 28.1 DEGREES REMARK 500 19 ALA A 692 N - CA - CB ANGL. DEV. = -9.8 DEGREES REMARK 500 20 ASP A 674 CB - CG - OD1 ANGL. DEV. = -6.1 DEGREES REMARK 500 20 ASP A 690 C - N - CA ANGL. DEV. = 15.9 DEGREES REMARK 500 20 SER A 691 CA - C - N ANGL. DEV. = -19.8 DEGREES REMARK 500 20 ALA A 692 C - N - CA ANGL. DEV. = 24.5 DEGREES REMARK 500 20 ALA A 692 N - CA - CB ANGL. DEV. = -10.1 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 ASP A 690 32.67 -82.59 REMARK 500 1 SER A 691 107.26 -44.16 REMARK 500 1 ALA A 692 176.13 -58.33 REMARK 500 1 SER A 737 179.73 -59.97 REMARK 500 1 THR A 738 18.17 -59.60 REMARK 500 1 ALA A 739 104.61 -58.49 REMARK 500 2 ALA A 646 22.82 -34.52 REMARK 500 2 SER A 647 -178.67 -50.27 REMARK 500 2 ASP A 648 27.49 -52.41 REMARK 500 2 CYS A 649 107.04 -51.04 REMARK 500 3 ALA A 646 25.62 -56.94 REMARK 500 3 SER A 647 -173.54 -49.18 REMARK 500 3 ASP A 648 29.85 -49.82 REMARK 500 3 CYS A 649 103.98 -49.88 REMARK 500 3 LEU A 658 -24.56 -34.92 REMARK 500 3 ASP A 690 -65.00 -103.45 REMARK 500 3 ARG A 734 -179.74 -69.62 REMARK 500 4 CYS A 649 104.53 -59.04 REMARK 500 4 SER A 736 -177.32 -56.42 REMARK 500 4 SER A 737 173.16 -53.04 REMARK 500 5 LEU A 658 -18.42 -41.80 REMARK 500 6 ALA A 646 20.93 -76.53 REMARK 500 6 SER A 647 178.99 -54.01 REMARK 500 6 ASP A 648 25.89 -58.70 REMARK 500 6 ASP A 690 -65.60 -90.15 REMARK 500 7 THR A 738 16.60 -63.82 REMARK 500 7 ALA A 739 104.31 -59.61 REMARK 500 8 ALA A 646 19.37 -67.11 REMARK 500 8 SER A 647 179.73 -56.34 REMARK 500 8 ASP A 648 17.07 -61.05 REMARK 500 9 GLU A 657 20.08 -79.16 REMARK 500 9 LEU A 658 -24.32 -39.52 REMARK 500 10 ASP A 648 17.93 -63.44 REMARK 500 10 ARG A 735 -179.50 -66.40 REMARK 500 11 SER A 647 105.18 -58.27 REMARK 500 11 LEU A 658 -39.74 -35.99 REMARK 500 11 ASP A 674 177.10 -59.35 REMARK 500 11 SER A 691 104.76 -165.82 REMARK 500 12 ALA A 713 -1.14 -59.81 REMARK 500 13 ALA A 646 15.39 -68.72 REMARK 500 13 LEU A 658 2.54 -57.13 REMARK 500 13 ALA A 692 109.29 -163.59 REMARK 500 14 LEU A 658 -36.06 -36.89 REMARK 500 15 LEU A 658 -33.52 -39.41 REMARK 500 16 LEU A 658 -18.69 -49.96 REMARK 500 16 THR A 738 17.57 -65.08 REMARK 500 17 ASP A 648 15.00 -63.92 REMARK 500 17 SER A 672 -8.14 -59.30 REMARK 500 17 ALA A 694 -8.15 -54.99 REMARK 500 17 SER A 736 -176.68 -54.78 REMARK 500 REMARK 500 THIS ENTRY HAS 62 RAMACHANDRAN OUTLIERS. 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 2 ARG A 689 0.09 SIDE CHAIN REMARK 500 3 ARG A 689 0.08 SIDE CHAIN REMARK 500 5 ARG A 650 0.08 SIDE CHAIN REMARK 500 6 ARG A 682 0.09 SIDE CHAIN REMARK 500 9 ARG A 682 0.08 SIDE CHAIN REMARK 500 9 ARG A 734 0.11 SIDE CHAIN REMARK 500 11 TYR A 719 0.08 SIDE CHAIN REMARK 500 11 ARG A 731 0.09 SIDE CHAIN REMARK 500 12 ARG A 731 0.08 SIDE CHAIN REMARK 500 12 ARG A 733 0.09 SIDE CHAIN REMARK 500 13 ARG A 682 0.11 SIDE CHAIN REMARK 500 13 TYR A 697 0.07 SIDE CHAIN REMARK 500 13 ARG A 734 0.09 SIDE CHAIN REMARK 500 14 TYR A 697 0.09 SIDE CHAIN REMARK 500 14 ARG A 707 0.08 SIDE CHAIN REMARK 500 15 ARG A 731 0.10 SIDE CHAIN REMARK 500 16 TYR A 697 0.07 SIDE CHAIN REMARK 500 17 ARG A 689 0.09 SIDE CHAIN REMARK 500 17 ARG A 707 0.14 SIDE CHAIN REMARK 500 20 ARG A 653 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34754 RELATED DB: BMRB REMARK 900 STRUCTURAL INSIGHTS REVEAL A HETEROTETRAMER BETWEEN ONCOGENIC K- REMARK 900 RAS4BG12V AND RGL2, A RALA/B ACTIVATOR DBREF 8AU4 A 643 740 UNP O15211 RGL2_HUMAN 643 740 SEQADV 8AU4 SER A 641 UNP O15211 EXPRESSION TAG SEQADV 8AU4 MET A 642 UNP O15211 EXPRESSION TAG SEQRES 1 A 100 SER MET GLY PRO GLY ALA SER ASP CYS ARG ILE ILE ARG SEQRES 2 A 100 VAL GLN MET GLU LEU GLY GLU ASP GLY SER VAL TYR LYS SEQRES 3 A 100 SER ILE LEU VAL THR SER GLN ASP LYS ALA PRO SER VAL SEQRES 4 A 100 ILE SER ARG VAL LEU LYS LYS ASN ASN ARG ASP SER ALA SEQRES 5 A 100 VAL ALA SER GLU TYR GLU LEU VAL GLN LEU LEU PRO GLY SEQRES 6 A 100 GLU ARG GLU LEU THR ILE PRO ALA SER ALA ASN VAL PHE SEQRES 7 A 100 TYR ALA MET ASP GLY ALA SER HIS ASP PHE LEU LEU ARG SEQRES 8 A 100 GLN ARG ARG ARG SER SER THR ALA THR HELIX 1 AA1 LEU A 658 GLY A 662 5 5 HELIX 2 AA2 LYS A 675 ASN A 687 1 13 HELIX 3 AA3 VAL A 693 SER A 695 5 3 HELIX 4 AA4 ASN A 716 MET A 721 1 6 SHEET 1 AA1 5 LYS A 666 VAL A 670 0 SHEET 2 AA1 5 ARG A 650 GLN A 655 -1 N ILE A 652 O ILE A 668 SHEET 3 AA1 5 ASP A 727 GLN A 732 1 O PHE A 728 N ARG A 653 SHEET 4 AA1 5 TYR A 697 LEU A 703 -1 N VAL A 700 O LEU A 729 SHEET 5 AA1 5 ARG A 707 ILE A 711 -1 O LEU A 709 N GLN A 701 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