PDB Short entry for 2ODG HEADER MEMBRANE PROTEIN, PROTEIN BINDING 22-DEC-06 2ODG TITLE COMPLEX OF BARRIER-TO-AUTOINTEGRATION FACTOR AND LEM-DOMAIN OF EMERIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: BARRIER-TO-AUTOINTEGRATION FACTOR; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 1-89; COMPND 5 SYNONYM: BREAKPOINT CLUSTER REGION PROTEIN 1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: EMERIN; COMPND 9 CHAIN: C; COMPND 10 FRAGMENT: RESIDUES 2-47; 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 CELLULAR_LOCATION: NUCLEUS; SOURCE 6 GENE: BANF1, BAF, BCRG1; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 CELLULAR_LOCATION: NUCLEUS; SOURCE 14 GENE: EMD, EDMD, STA; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INNER NUCLEAR MEMBRANE PROTEIN, LEM-DOMAIN BAF MULTIDIMENSIONAL NMR KEYWDS 2 DIPOLAR COUPLINGS, MEMBRANE PROTEIN, PROTEIN BINDING EXPDTA SOLUTION NMR AUTHOR G.M.CLORE,M.CAI REVDAT 5 27-DEC-23 2ODG 1 REMARK REVDAT 4 16-MAR-22 2ODG 1 REMARK SEQADV REVDAT 3 24-FEB-09 2ODG 1 VERSN REVDAT 2 22-MAY-07 2ODG 1 JRNL REVDAT 1 13-MAR-07 2ODG 0 JRNL AUTH M.CAI,Y.HUANG,J.Y.SUH,J.M.LOUIS,R.GHIRLANDO,R.CRAIGIE, JRNL AUTH 2 G.M.CLORE JRNL TITL SOLUTION NMR STRUCTURE OF THE BARRIER-TO-AUTOINTEGRATION JRNL TITL 2 FACTOR-EMERIN COMPLEX. JRNL REF J.BIOL.CHEM. V. 282 14525 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17355960 JRNL DOI 10.1074/JBC.M700576200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES WERE CALCULATED BY REMARK 3 CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (SCHWIETERS & CLORE REMARK 3 (2001) J.MAGN.RESON 152, 288-302). THE TARGET FUNCTIONS REMARK 3 COMPRISES TERMS FOR NOE RESTRAINTS, SIDECHAIN TORSION ANGLE REMARK 3 RESTRAINTS, RESIDUAL DIPOLAR COUPLING RESTRAINTS (CLORE ET AL. REMARK 3 J.MAGN.RESON. 131, 159-162 (1998); J.MAGN.RESON.133, 216- REMARK 3 221(1998)), A RADIUS OF GYRATION TERM (KUSZEWSKI ET AL. REMARK 3 J.AM.CHEM.SOC. 121, 2337-2338 (1999)), A QUARTIC VAN DER WAALS REMARK 3 REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229, 129-136), REMARK 3 AND A TORSION ANGLE CONFORMATIONAL DATABASE POTENTIAL OF MEAN REMARK 3 FORCE (CLORE AND KUSZEWSKI 2002) J.AM.CHEM.SOC 124, 2866-2867). REMARK 3 THE STARTING COORDINATE COME FROM THE NMR STRUCTURE OF THE BAF REMARK 3 DIMER (1QCK; KUSZEWSKI ET AL. J.AM.CHEM.SOC.121, 2337-2338(1999)) REMARK 3 AND THE LEM-DOMAIN OF EMERIN (PDB ID 2ODC; CAI ET AL) THE REMARK 3 BACKBONE COORDINATES AND NON-INTERFACIAL SIDECHAINS ARE TREATED REMARK 3 AS RIGID BODIES THROUGHOUT WITH THE BAF DIMER HELD FIXED, THE REMARK 3 MOLECULES ALLOWED TO ROTATE AND TRANSLATE, AND THE AXIS OF THE REMARK 3 SINGLE DIPOLAR COUPLING ALIGNMENT TENSOR FREE TO ROTATE. THE REMARK 3 INTERFACIAL SIDECHAINS ARE GIVEN FULL TORSIONAL DEGREES OF REMARK 3 FREEDOM. REMARK 4 REMARK 4 2ODG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 7 REMARK 7 IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS REMARK 7 DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING REMARK 7 STRUCTURES AND THE MEAN COORDINATE POSITIONS. IT IS REMARK 7 IMPORTANT TO NOTE THAT THE VALUES GIVEN FOR THE BACKBONE REMARK 7 ATOMS AND NON-INTERFACIAL SIDECHAINS PROVIDE ONLY A REMARK 7 MEASURE OF THE PRECISION WITH WHICH THE RELATIVE REMARK 7 ORIENTATION OF THE TWO PROTEINS HAVE BEEN DETERMINED AND REMARK 7 DOES NOT TAKE INTO ACCOUNT THE ERRORS IN THE NMR REMARK 7 COORDINATES OF THE FREE BAF DIMER AND THE LEM-DOMAIN REMARK 7 OF EMERIN. REMARK 7 STRUCTURAL STATISTICS: REMARK 7 --------------------------------------------------------- REMARK 7 RMS DEVIATIONS FROM EXPT RESTRAINTS REMARK 7 NOES (122) 0.016 A REMARK 7 SIDE-CHAIN TORSION ANGLES (46) 0.025 DEG REMARK 7 1DNH DIPOLAR COUPLING R-FACTORS (CLORE AND GARRETT (1999) REMARK 7 J. AM. CHEM. SOC. 121, 9008-9012): REMARK 7 BAF (54X2) 15.2% LEM-DOMAIN: 14.8% REMARK 7 -------------------------------------------------------- REMARK 7 COORDINATE PRECISION REMARK 7 BACKBONE: 0.13(+/-0.06) A REMARK 7 INTERFACIAL SIDE-CHAIN HEAVY ATOMS: 1.02(+/-0.02) A REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000040996. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303.00 REMARK 210 PH : 6.50 REMARK 210 IONIC STRENGTH : 50 MM POTASSIUM PHOSPHATE 200 MM REMARK 210 NACL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DOUBLE AND TRIPLE RESONANCE FOR REMARK 210 ASSIGNMENT OF PROTEIN; REMARK 210 QUANTITATIVE J CORRELATION FOR REMARK 210 COUPLING CONSTANTS; 3D REMARK 210 HETREONUCLEAR-SEPARATED NOE REMARK 210 EXPERIMENTS; 2D HETERONUCLEAR REMARK 210 FOR DIPOLAR COUPLING REMARK 210 MEASUREMENTS IN LIQUID REMARK 210 CRYSTALLINE MEDIUM OF PHAGE PF1 REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XPLOR-NIH REMARK 210 METHOD USED : CONJOINED RIGID BODY/TORSION REMARK 210 ANGLE SIMULATED ANNEALING REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 180 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : RESTRAINED REGULARIZED MEAN REMARK 210 STRUCTURE 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 OD1 ASP B 55 H LEU B 58 1.35 REMARK 500 OD1 ASP A 55 H LEU A 58 1.39 REMARK 500 O PHE C 39 HG1 THR C 43 1.48 REMARK 500 O CYS B 85 H LEU B 89 1.49 REMARK 500 O MET B 1 H THR B 3 1.51 REMARK 500 O MET A 1 H THR A 3 1.51 REMARK 500 O VAL C 27 H ARG C 31 1.60 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 PHE B 88 CB PHE B 88 CG 0.162 REMARK 500 PHE B 88 CG PHE B 88 CD1 0.118 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 2 61.78 -56.32 REMARK 500 PRO A 14 159.98 -39.99 REMARK 500 PHE A 39 74.29 -106.39 REMARK 500 LYS A 54 19.43 56.87 REMARK 500 THR B 2 61.68 -55.98 REMARK 500 PRO B 14 160.04 -39.99 REMARK 500 PHE B 39 74.16 -107.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ODC RELATED DB: PDB REMARK 900 LEM-DOMAIN OF THE NUCLEAR ENVELOPE PROTEIN EMERIN DBREF 2ODG A 1 89 UNP O75531 BAF_HUMAN 1 89 DBREF 2ODG B 1 89 UNP O75531 BAF_HUMAN 1 89 DBREF 2ODG C 2 47 UNP P50402 EMD_HUMAN 2 47 SEQADV 2ODG HIS C 1 UNP P50402 CLONING ARTIFACT SEQRES 1 A 89 MET THR THR SER GLN LYS HIS ARG ASP PHE VAL ALA GLU SEQRES 2 A 89 PRO MET GLY GLU LYS PRO VAL GLY SER LEU ALA GLY ILE SEQRES 3 A 89 GLY GLU VAL LEU GLY LYS LYS LEU GLU GLU ARG GLY PHE SEQRES 4 A 89 ASP LYS ALA TYR VAL VAL LEU GLY GLN PHE LEU VAL LEU SEQRES 5 A 89 LYS LYS ASP GLU ASP LEU PHE ARG GLU TRP LEU LYS ASP SEQRES 6 A 89 THR CYS GLY ALA ASN ALA LYS GLN SER ARG ASP CYS PHE SEQRES 7 A 89 GLY CYS LEU ARG GLU TRP CYS ASP ALA PHE LEU SEQRES 1 B 89 MET THR THR SER GLN LYS HIS ARG ASP PHE VAL ALA GLU SEQRES 2 B 89 PRO MET GLY GLU LYS PRO VAL GLY SER LEU ALA GLY ILE SEQRES 3 B 89 GLY GLU VAL LEU GLY LYS LYS LEU GLU GLU ARG GLY PHE SEQRES 4 B 89 ASP LYS ALA TYR VAL VAL LEU GLY GLN PHE LEU VAL LEU SEQRES 5 B 89 LYS LYS ASP GLU ASP LEU PHE ARG GLU TRP LEU LYS ASP SEQRES 6 B 89 THR CYS GLY ALA ASN ALA LYS GLN SER ARG ASP CYS PHE SEQRES 7 B 89 GLY CYS LEU ARG GLU TRP CYS ASP ALA PHE LEU SEQRES 1 C 47 HIS ASP ASN TYR ALA ASP LEU SER ASP THR GLU LEU THR SEQRES 2 C 47 THR LEU LEU ARG ARG TYR ASN ILE PRO HIS GLY PRO VAL SEQRES 3 C 47 VAL GLY SER THR ARG ARG LEU TYR GLU LYS LYS ILE PHE SEQRES 4 C 47 GLU TYR GLU THR GLN ARG ARG ARG HELIX 1 1 SER A 4 VAL A 11 1 8 HELIX 2 2 PRO A 19 LEU A 23 5 5 HELIX 3 3 GLY A 27 ARG A 37 1 11 HELIX 4 4 LYS A 41 LEU A 52 1 12 HELIX 5 5 ASP A 55 GLY A 68 1 14 HELIX 6 6 ASN A 70 LEU A 89 1 20 HELIX 7 7 SER B 4 VAL B 11 1 8 HELIX 8 8 PRO B 19 LEU B 23 5 5 HELIX 9 9 GLY B 27 ARG B 37 1 11 HELIX 10 10 LYS B 41 LEU B 52 1 12 HELIX 11 11 ASP B 55 GLY B 68 1 14 HELIX 12 12 ASN B 70 LEU B 89 1 20 HELIX 13 13 ASP C 2 LEU C 7 5 6 HELIX 14 14 SER C 8 TYR C 19 1 12 HELIX 15 15 VAL C 27 ARG C 47 1 21 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 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