HEADER TRANSCRIPTION 25-MAR-24 8YTF TITLE CRYSTAL STRUCTURES OF HUMAN IRF2BP2 RING DOMAIN IN COMPLEX WITH VGLL4 TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERFERON REGULATORY FACTOR 2-BINDING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RING DOMAIN; COMPND 5 SYNONYM: IRF-2-BINDING PROTEIN 2,IRF-2BP2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: TRANSCRIPTION COFACTOR VESTIGIAL-LIKE PROTEIN 4; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: VGL-4; 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: IRF2BP2; 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: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS IRF2BP2, RING DOMAIN, VGLL4, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR G.C.WANG,J.P.DING REVDAT 1 20-NOV-24 8YTF 0 JRNL AUTH G.C.WANG,J.P.DING JRNL TITL IRF2BP2 RECOGNIZES AND BIND TO A CONSERVED RXSVI SEQUENCE JRNL TITL 2 MOTIF OF PROTEIN PARTNERS AND INTERACTS WITH ZBTB16 TO JRNL TITL 3 REGULATE MEGAKARYOCYTIC DIFFERENTIATION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 11054 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 519 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 23.4300 - 2.5300 0.99 2806 120 0.1640 0.1718 REMARK 3 2 2.5300 - 2.0100 1.00 2661 135 0.1507 0.1767 REMARK 3 3 2.0100 - 1.7500 0.99 2620 127 0.1332 0.1630 REMARK 3 4 1.7500 - 1.5900 0.95 2448 137 0.1398 0.1795 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 662 REMARK 3 ANGLE : 1.064 900 REMARK 3 CHIRALITY : 0.057 102 REMARK 3 PLANARITY : 0.011 117 REMARK 3 DIHEDRAL : 6.291 89 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8YTF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 28-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1300046332. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9752 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11169 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : 12.30 REMARK 200 R MERGE FOR SHELL (I) : 0.32700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% 2-PROPONAL, 0.1 M MES (PH 6.0) AND REMARK 280 20% (W/V) PEG MME 2000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 16.68600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.88050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.60450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.88050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.68600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.60450 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 TOTAL BURIED SURFACE AREA: 900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL 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 GLY A 496 REMARK 465 GLY A 577 REMARK 465 ASP A 578 REMARK 465 CYS B 7 REMARK 465 ALA B 8 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH A 702 O HOH A 781 1.82 REMARK 500 O HOH A 780 O HOH A 815 1.89 REMARK 500 O HOH A 778 O HOH A 788 1.90 REMARK 500 O HOH A 795 O HOH A 808 1.90 REMARK 500 O HOH A 773 O HOH A 784 1.91 REMARK 500 O HOH A 781 O HOH A 815 1.93 REMARK 500 O HOH A 784 O HOH A 819 2.12 REMARK 500 O HOH A 751 O HOH A 798 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 751 O HOH A 754 3544 1.81 REMARK 500 O HOH A 742 O HOH A 796 3544 2.05 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 THR A 500 148.30 -171.89 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 603 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 497 N REMARK 620 2 SER A 497 O 87.1 REMARK 620 3 HIS A 510 NE2 100.2 15.5 REMARK 620 4 HOH A 741 O 170.2 83.3 70.6 REMARK 620 5 HOH A 744 O 94.6 88.0 95.1 83.4 REMARK 620 6 HOH A 774 O 89.8 86.4 78.4 91.3 172.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 601 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 506 SG REMARK 620 2 CYS A 509 SG 107.3 REMARK 620 3 CYS A 530 SG 116.5 109.0 REMARK 620 4 CYS A 533 SG 113.0 109.9 100.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 521 SG REMARK 620 2 HIS A 527 ND1 118.3 REMARK 620 3 CYS A 549 SG 111.5 102.9 REMARK 620 4 CYS A 555 SG 110.3 103.9 109.3 REMARK 620 N 1 2 3 DBREF 8YTF A 497 578 UNP Q7Z5L9 I2BP2_HUMAN 497 578 DBREF 8YTF B 1 8 UNP Q14135 VGLL4_HUMAN 161 168 SEQADV 8YTF GLY A 496 UNP Q7Z5L9 EXPRESSION TAG SEQRES 1 A 83 GLY SER LEU ALA THR SER ALA PRO LEU CYS CYS THR LEU SEQRES 2 A 83 CYS HIS GLU ARG LEU GLU ASP THR HIS PHE VAL GLN CYS SEQRES 3 A 83 PRO SER VAL PRO SER HIS LYS PHE CYS PHE PRO CYS SER SEQRES 4 A 83 ARG GLN SER ILE LYS GLN GLN GLY ALA SER GLY GLU VAL SEQRES 5 A 83 TYR CYS PRO SER GLY GLU LYS CYS PRO LEU VAL GLY SER SEQRES 6 A 83 ASN VAL PRO TRP ALA PHE MET GLN GLY GLU ILE ALA THR SEQRES 7 A 83 ILE LEU ALA GLY ASP SEQRES 1 B 8 ARG PRO SER VAL ILE THR CYS ALA HET ZN A 601 1 HET ZN A 602 1 HET ZN A 603 1 HETNAM ZN ZINC ION FORMUL 3 ZN 3(ZN 2+) FORMUL 6 HOH *128(H2 O) HELIX 1 AA1 CYS A 530 GLY A 542 1 13 HELIX 2 AA2 ALA A 543 GLY A 545 5 3 HELIX 3 AA3 MET A 567 ALA A 576 1 10 SHEET 1 AA1 2 VAL A 519 GLN A 520 0 SHEET 2 AA1 2 LYS A 528 PHE A 529 -1 O PHE A 529 N VAL A 519 LINK N SER A 497 ZN ZN A 603 1555 1555 2.04 LINK O SER A 497 ZN ZN A 603 1555 1555 2.08 LINK SG CYS A 506 ZN ZN A 601 1555 1555 2.35 LINK SG CYS A 509 ZN ZN A 601 1555 1555 2.34 LINK NE2 HIS A 510 ZN ZN A 603 1555 1655 2.19 LINK SG CYS A 521 ZN ZN A 602 1555 1555 2.35 LINK ND1 HIS A 527 ZN ZN A 602 1555 1555 2.10 LINK SG CYS A 530 ZN ZN A 601 1555 1555 2.37 LINK SG CYS A 533 ZN ZN A 601 1555 1555 2.27 LINK SG CYS A 549 ZN ZN A 602 1555 1555 2.35 LINK SG CYS A 555 ZN ZN A 602 1555 1555 2.27 LINK ZN ZN A 603 O HOH A 741 1555 1555 2.24 LINK ZN ZN A 603 O HOH A 744 1555 1555 2.09 LINK ZN ZN A 603 O HOH A 774 1555 1555 2.30 CRYST1 33.372 43.209 55.761 90.00 90.00 90.00 P 21 21 21 4 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 0.029965 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023143 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017934 0.00000