HEADER TRANSCRIPTION 22-DEC-15 2NAA TITLE NSD1-PHD_5-C5HCH TANDEM DOMAIN STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-36 AND H4 COMPND 3 LYSINE-20 SPECIFIC; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 2014-2104; COMPND 6 SYNONYM: H3-K36-HMTASE, H4-K20-HMTASE, NUCLEAR RECEPTOR-BINDING SET COMPND 7 DOMAIN-CONTAINING PROTEIN 1, NR-BINDING SET DOMAIN-CONTAINING COMPND 8 PROTEIN; COMPND 9 EC: 2.1.1.43; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: NSD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PETM11 KEYWDS NSD1, PHD5C5HCH, PHD FINGER, TANDEM, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR A.BERARDI,G.QUILICI,D.SPILIOTOPOULOS,G.MUSCO REVDAT 3 14-JUN-23 2NAA 1 REMARK SEQADV LINK REVDAT 2 04-MAY-16 2NAA 1 JRNL REVDAT 1 09-MAR-16 2NAA 0 JRNL AUTH A.BERARDI,G.QUILICI,D.SPILIOTOPOULOS,M.A.CORRAL-RODRIGUEZ, JRNL AUTH 2 F.MARTIN-GARCIA,M.DEGANO,G.TONON,M.GHITTI,G.MUSCO JRNL TITL STRUCTURAL BASIS FOR PHDVC5HCHNSD1-C2HRNIZP1 INTERACTION: JRNL TITL 2 IMPLICATIONS FOR SOTOS SYNDROME. JRNL REF NUCLEIC ACIDS RES. V. 44 3448 2016 JRNL REFN ISSN 0305-1048 JRNL PMID 26896805 JRNL DOI 10.1093/NAR/GKW103 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.3, ARIA REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2NAA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000104619. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 6.3 REMARK 210 IONIC STRENGTH : 0.150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3 MM PROTEIN_1, 90% H2O/10% REMARK 210 D2O; 0.3 MM [U-99% 13C; U-99% REMARK 210 15N] PROTEIN_1, 90% H2O/10% D2O; REMARK 210 0.3 MM [U-99% 15N] PROTEIN_1, 90% REMARK 210 H2O/10% D2O; 0.3 MM PROTEIN_1, REMARK 210 100% D2O; 0.3 MM [U-99% 13C; U- REMARK 210 99% 15N] PROTEIN_1, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 3D CBCA(CO)NH; 3D C(CO)NH; 3D REMARK 210 HNCO; 3D HNCA; 3D H(CCO)NH; 3D REMARK 210 HCCH-TOCSY; 3D HNHA; 3D HNCACB; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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 OE1 GLU A 6 HZ1 LYS A 28 1.57 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 MET A 3 -47.98 -159.69 REMARK 500 1 ASP A 7 51.15 -103.97 REMARK 500 2 MET A 3 24.55 -140.32 REMARK 500 2 LYS A 22 34.77 -95.13 REMARK 500 3 MET A 3 20.99 -154.54 REMARK 500 4 ALA A 2 74.48 -112.31 REMARK 500 4 PRO A 67 26.44 -76.25 REMARK 500 5 ALA A 2 -70.22 67.53 REMARK 500 5 HIS A 93 50.72 -109.11 REMARK 500 6 GLN A 17 83.65 66.57 REMARK 500 6 PRO A 67 20.04 -74.43 REMARK 500 6 HIS A 93 51.24 -117.42 REMARK 500 7 MET A 3 71.03 58.34 REMARK 500 8 MET A 3 -79.97 69.47 REMARK 500 8 LYS A 22 37.35 -82.76 REMARK 500 8 PRO A 67 7.96 -69.87 REMARK 500 8 HIS A 93 57.79 -112.62 REMARK 500 10 GLU A 4 -164.68 66.45 REMARK 500 10 ASP A 7 51.70 -109.09 REMARK 500 10 PRO A 67 28.47 -70.93 REMARK 500 10 THR A 91 21.11 -78.12 REMARK 500 11 GLN A 17 84.72 63.31 REMARK 500 11 PRO A 67 29.55 -73.85 REMARK 500 12 MET A 3 64.76 -109.99 REMARK 500 12 PRO A 48 0.14 -69.31 REMARK 500 12 PRO A 67 25.25 -75.08 REMARK 500 14 ALA A 2 61.16 -118.12 REMARK 500 14 ASP A 7 50.03 -116.25 REMARK 500 14 LYS A 22 32.92 -89.05 REMARK 500 14 HIS A 93 55.64 -102.22 REMARK 500 15 ALA A 2 69.00 -113.07 REMARK 500 15 MET A 3 -66.54 -90.88 REMARK 500 15 LYS A 22 38.55 -92.53 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 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 9 SG REMARK 620 2 CYS A 12 SG 109.2 REMARK 620 3 HIS A 31 ND1 108.0 111.0 REMARK 620 4 CYS A 34 SG 108.0 109.9 110.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 21 SG REMARK 620 2 CYS A 26 SG 107.9 REMARK 620 3 CYS A 47 SG 108.9 110.3 REMARK 620 4 HIS A 50 NE2 109.8 109.5 110.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 103 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 52 SG REMARK 620 2 CYS A 55 SG 106.7 REMARK 620 3 CYS A 71 SG 107.9 111.3 REMARK 620 4 HIS A 74 ND1 108.9 111.9 109.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 104 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 63 SG REMARK 620 2 CYS A 66 SG 108.8 REMARK 620 3 CYS A 90 SG 109.4 111.0 REMARK 620 4 HIS A 93 NE2 108.6 110.0 109.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 104 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25933 RELATED DB: BMRB REMARK 900 RELATED ID: 2NAB RELATED DB: PDB DBREF 2NAA A 4 94 UNP O88491 NSD1_MOUSE 2014 2104 SEQADV 2NAA GLY A 1 UNP O88491 EXPRESSION TAG SEQADV 2NAA ALA A 2 UNP O88491 EXPRESSION TAG SEQADV 2NAA MET A 3 UNP O88491 EXPRESSION TAG SEQRES 1 A 94 GLY ALA MET GLU ARG GLU ASP GLU CYS PHE SER CYS GLY SEQRES 2 A 94 ASP ALA GLY GLN LEU VAL SER CYS LYS LYS PRO GLY CYS SEQRES 3 A 94 PRO LYS VAL TYR HIS ALA ASP CYS LEU ASN LEU THR LYS SEQRES 4 A 94 ARG PRO ALA GLY LYS TRP GLU CYS PRO TRP HIS GLN CYS SEQRES 5 A 94 ASP VAL CYS GLY LYS GLU ALA ALA SER PHE CYS GLU MET SEQRES 6 A 94 CYS PRO SER SER PHE CYS LYS GLN HIS ARG GLU GLY MET SEQRES 7 A 94 LEU PHE ILE SER LYS LEU ASP GLY ARG LEU SER CYS THR SEQRES 8 A 94 GLU HIS ASP HET ZN A 101 1 HET ZN A 102 1 HET ZN A 103 1 HET ZN A 104 1 HETNAM ZN ZINC ION FORMUL 2 ZN 4(ZN 2+) HELIX 1 1 CYS A 47 GLN A 51 5 5 SHEET 1 A 2 LEU A 18 SER A 20 0 SHEET 2 A 2 VAL A 29 HIS A 31 -1 O TYR A 30 N VAL A 19 SHEET 1 B 2 LEU A 79 ILE A 81 0 SHEET 2 B 2 LEU A 88 CYS A 90 -1 O SER A 89 N PHE A 80 LINK SG CYS A 9 ZN ZN A 101 1555 1555 2.30 LINK SG CYS A 12 ZN ZN A 101 1555 1555 2.30 LINK SG CYS A 21 ZN ZN A 102 1555 1555 2.29 LINK SG CYS A 26 ZN ZN A 102 1555 1555 2.29 LINK ND1 HIS A 31 ZN ZN A 101 1555 1555 2.01 LINK SG CYS A 34 ZN ZN A 101 1555 1555 2.31 LINK SG CYS A 47 ZN ZN A 102 1555 1555 2.30 LINK NE2 HIS A 50 ZN ZN A 102 1555 1555 2.00 LINK SG CYS A 52 ZN ZN A 103 1555 1555 2.29 LINK SG CYS A 55 ZN ZN A 103 1555 1555 2.30 LINK SG CYS A 63 ZN ZN A 104 1555 1555 2.29 LINK SG CYS A 66 ZN ZN A 104 1555 1555 2.29 LINK SG CYS A 71 ZN ZN A 103 1555 1555 2.29 LINK ND1 HIS A 74 ZN ZN A 103 1555 1555 2.00 LINK SG CYS A 90 ZN ZN A 104 1555 1555 2.30 LINK NE2 HIS A 93 ZN ZN A 104 1555 1555 1.99 SITE 1 AC1 4 CYS A 9 CYS A 12 HIS A 31 CYS A 34 SITE 1 AC2 4 CYS A 21 CYS A 26 CYS A 47 HIS A 50 SITE 1 AC3 4 CYS A 52 CYS A 55 CYS A 71 HIS A 74 SITE 1 AC4 4 CYS A 63 CYS A 66 CYS A 90 HIS A 93 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