NUCLEIC ACID DATABASE NEWSLETTER -------------------------------- Number 11. April 1994. C------W C------W C--------W NNN NNN DDDDDD BBBBBBB C--------W C--------W NNNN NNN DDDDDDDD BBBBBBBBB C--------W C-------W NNNNN NNN DDD DDD BBB BBB C-------W C----W NNN NN NNN DDD DDD BBBBBBB C----W W NNN NNNNN DDD DDD BBB BBB W W--C NNN NNNN DDDDDDDD BBBBBBBBB W--C W-----C NNN NNN DDDDDD BBBBBBB W-----C W--------C W--------C W---------C W---------C W--------C W--------C W-----C THE NUCLEIC ACID DATABASE: W-----C C -------------------------- C C--W C--W C------W A RELATIONAL DATABASE OF NUCLEIC C------W C--------W ACID CRYSTAL STRUCTURES C--------W C--------W C--------W NDB, A RELATIONAL DATABASE: -------------------------- The Nucleic Acid Database (NDB) is a relational database, which is designed to facilitate the easy search for nucleic acid structures using any of the stored primary or derived structural features. Reports can then be created describing any properties of the selected structures. The reports available via the electronic mail server represent some examples of the kinds of tables that can be produced. Generally, each report includes a column for the NDB structure ID, and each row describes the selected features for the structure whose ID appears in the first column. Given the power of the relational database system, any set of structures can be selected, and any available information about them can be collected. The released reports give selected examples, but more specialized and sophisticated reports can be produced. GETTING STARTED WITH NDB: ------------------------ If you have never received a newsletter before, send the following e-mail message to receive complete access information. Please note that this message is read and replied to by a computer, so the subject line must be exactly as it appears here: To: ndblib@ndbserver.rutgers.edu Subject: send access from newsletter To get personal help, send a message to this address: ndbadmin@ndbserver.rutgers.edu NEW STRUCTURES: -------------- The current release consists of updated tables describing the 256 DNA, RNA, and tRNA structures now contained in the database. Coordinates are available for 204 of these structures. We will also release information on 35 protein/DNA complexes. The coordinates for 22 of these structures are available. The following new structures, with coordinates, have been added to the database: ARL048 G.A.Leonard, K.E.McAuley-Hecht, S.Ebel, D.M.Lough, T.Brown, W.N.Hunter 5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*AP*GP*CP*G)-3' BDLB53 S.L.Ginell, J.Vojtechovsky, B.Gaffney, R.Jones, H.M.Berman 5'-D(*CP*GP*AP*GP*AP*AP*TP*TP*CP*(M)GP*CP*G)-3' DDH037 S.Kamitori, F.Takusagawa 5'-D(*GP*AP*AP*GP*CP*TP*TP*C)-3', ACTINOMYCIN D ZDFB36 A.R.Cervi, A.Guy, G.A.Leonard, R.Teoule, W.N.Hunter 5'-D(*CP*GP*CP*GP*(M)CP*G)-3' ZDFB37 G.P.Schroth, T.F.Kagawa, P.Shing Ho 5'-D(*(M)CP*GP*GP*GP*(M)CP*G)-3' The bibliographic information for the following structures is available: DDFS42 H.Zhang, Y.-G.Gao, G.A.Van Der Marel, J.H.Van Boom, A.H.-J.Wang 5'-D(*CP*GP*)-ARA(*CP*)-D(*GP*CP*G)-3', DAUNORUBICIN AND HCHO DDFS43 H.Zhang, Y.-G.Gao, G.A.Van Der Marel, J.H.Van Boom, A.H.-J.Wang 5'-D(*CP*AP*)-ARA(*CP*)-D(*GP*TP*G)-3', DOXORUBICIN AND HCHO GDLB24 Y.-G.Gao, M.Sriram, W.A.Denny, A.H.-J.Wang 5'-D(*CP*GP*CP*(E)GP*AP*AP*TP*TP*CP*GP*CP*G)-3', SN6999 ZDFB34 V.D.Kumar, I.T.Weber 5'-D(*CP*GP*CP*IP*CP*G)-3' Coordinates for the following structures have been released: ADJ050 B.Ramakrishnan, M.Sundaralingam 5'-D(*GP*CP*GP*GP*GP*CP*CP*CP*GP*C)-3', ORTHORHOMBIC ADJ051 B.Ramakrishnan, M.Sundaralingam 5'-D(*GP*CP*GP*GP*GP*CP*CP*CP*GP*C)-3', HEXAGONAL GDL014 L.Tabernero, N.Verdaguer, M.Coll, I.Fita, G.A.Van Der Marel, J.H.Van Boom, A.Rich, J.Aymami 5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3', NETROPSIN GDL021 M.Sriram, G.A.Van Der Marel, H.L.P.F.Roelen, J.H.Van Boom, A.H.-J.Wang 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', HOECHST 33342 GDL022 M.Sriram, G.A.Van Der Marel, H.L.P.F.Roelen, J.H.Van Boom, A.H.-J.Wang 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', HOECHST 33258 GDLB19 M.Sriram, G.A.Van Der Marel, H.L.P.F.Roelen, J.H.Van Boom, A.H.-J.Wang 5'-D(*CP*GP*CP*(E)GP*AP*AP*TP*TP*CP*GP*CP*G)-3', HOECHST 233258 GDLB20 M.Sriram, G.A.Van Der Marel, H.L.P.F.Roelen, J.H.Van Boom, A.H.-J.Wang 5'-D(*CP*GP*CP*(E)GP*AP*AP*TP*TP*CP*GP*CP*G)-3', HOECHST 233342 Coordinates for the following Protein/DNA complexes have been released: --------------------- The coordinates of these structures are available in NDB format. All coordinates for the nucleic acids are listed in front of the protein coordinates. The original residue numbers of each residue can be found in columns 74-77 of each coordinate file. PDE001 Y.Kim, J.C.Grable, R.Love, P.J.Greene J.M.Rosenberg ECO RI ENDONUCLEASE-DNA COMPLEX PDE002 F.K.Winkler, D.W.Banner, C.Oefner, D.Tsernoglou, R.S.Brown, S.P.Heathman, R.K.Bryan, P.D.Martin, K.Petratos, K.S.Wilson ECO RV ENDONUCLEASE-DNA COMPLEX PDE003 F.K.Winkler, D.W.Banner, C.Oefner, D.Tsernoglou, R.S.Brown, S.P.Heathman, R.K.Bryan, P.D.Martin, K.Petratos, K.S.Wilson ECO RV ENDONUCLEASE-DNA COMPLEX PDE005 S.A.Weston, A.Lahm, D.Suck DEOXYRIBONUCLEASE I (DNASE I)-DNA COMPLEX PDE006 A.Lahm, D.Suck DEOXYRIBONUCLEASE I (DNASE I)-DNA COMPLEX PDR001 A.Mondragon, S.C.Harrison 434 CRO-DNA COMPLEX PDR003 R.G.Brennan, S.L.Roderick, Y.Takeda, B.W.Matthews LAMBDA CRO-DNA COMPLEX PDR004 A.K.Aggarwal, D.W.Rodgers, M.Drottar, M.Ptashne, S.C.Harrison 434 REPRESSOR-OPERATOR COMPLEX PDR006 S.C.Schultz, G.C.Shields, T.A.Steitz CATABOLITE GENE ACTIVATOR-DNA COMPLEX PDR007 S.R.Jordan, C.O.Pabo LAMBDA REPRESSOR-OPERATOR COMPLEX PDR008 W.S.Somers, S.E.V.Phillips E. COLI MET REPRESSOR-OPERATOR-COMPLEX PDR009 Z.Otwinowski, R.W.Schevitz, R.G.Zhang, C.L.Lawson, A.Joachimiak, R.Q.Mamorstein, B.F.Luisi, P.B.Sigler TRP REPRESSOR-OPERATOR COMPLEX PDR010 L.J.Beamer, C.O.Pabo LAMBDA REPRESSOR-OPERATOR COMPLEX PDR011 L.J.W.Shimon, S.C.Harrison 434 REPRESSOR-OPERATOR COMPLEX PDRC01 B.F.Luisi, W.X.Xu, Z.Otwinowski, L.P.Freedman, K.R.Yamamoto, P.B.Sigler GLUCOCORTICOID RECEPTOR-DNA COMPLEX PDT002 T.E.Ellenberger, C.J.Brandl, K.Struhl, S.C.Harrison GCN4-DNA COMPLEX PDT003 R.Marmorstein, M.Carey, M.Ptashne, S.C.Harrison GAL4-DNA COMPLEX PDT004 C.R.Kissinger, B.Liu, E.Martin-Blanco, T.B.Kornberg C.O.Pabo ENGRAILED HOMEODOMAIN-DNA COMPLEX PDT006 N.P.Pavletich, C.O.Pabo ZIF268-DNA COMPLEX PDV001 R.S.Hegde, S.R.Grossman, L.A.Laimins, P.B.Sigler BOVINE PAPILLOMAVIRUS-1 E2-DNA COMPLEX PRV001 G.Z.Chen, C.Stauffacher, Y.Li, T.Schmidt, W.Bomu, G.Kamer, M.Shanks, G.Lomonossoff, J.E.Johnson BEAN POD MOTTLE VIRUS-(PROTEIN-RNA COMPLEX) PTR001 M.A.Rould, J.J.Perona, D.Soell, T.A.Steitz GLUTAMINYL-TRNA SYNTHETASE (GLN RS)-TRNA-GLN COMPLEX ------------------------------------------------------------------------------ The bibliographic information for the following Protein/DNA structures is available: PDE004 L.S.Beese, V.Derbyshire, T.A.Steitz KLENOW FRAGMENT-DNA COMPLEX PDE007 J.-A.Feng, R.C.Johnson, R.E.Dickerson HIN RECOMBINASE-DNA COMPLEX PDEB08 S.Klimasauskas, S.Kumar, R.J.Roberts, X.Cheng HHAL METHYLTRANSFERASE-DNA COMPLEX PDR002 C.Wollberger, Y.Dong, M.Ptashne, S.C.Harrison 434 CRO-DNA COMPLEX PDR005 J.E.Anderson, M.Ptashne, S.C.Harrison 434 CRO-DNA COMPLEX PDR012 B.E.Raumann, M.A.Rould, C.O.Pabo, R.T.Sauer ARC REPRESSOR-OPERATOR COMPLEX PDR013 C.L.Lawson, J.Carey TRP REPRESSOR-OPERATOR COMPLEX PDT005 C.Wolberger, A.K.Vershon, B.Liu, A.D.Johnson, C.O.Pabo MAT-ALPHA2 HOMEODOMAIN-DNA COMPLEX PDT007 P.Koenig and T.J.Richmond GCN4-DNA COMPLEX PDT008 N.P.Pavletich, C.O.Pabo FIVE FINGER GLI-DNA COMPLEX PDT009 J.L.Kim, D.B.Nikolov, S.K.Burley TATA-BOX BINDING POLYPEPTIDE (TBP)-DNA COMPLEX PDT010 T.A.Ceska, M.Lamers, P.Monaci, A.Nicosia, R.Cortese D.Suck LFB1/HNF1 HOMEODOMAIN-DNA COMPLEX PDV002 R.McKenna, D.Xia, P.Willingmann, L.L.Ilag, S.Krishnaswamy, M.G.Rossmann, N.H.Olson, T.S.Baker, N.L.Incardona BACTERIOPHAGE PHIX174-DNA COMPLEX Coordinates are released only after authorization by the Brookhaven Protein Data Bank. COORDINATE FILES NOW AVAILABLE IN PDB (BROOKHAVEN PROTEIN DATA BANK) FORMAT: --------------------------------------------------------------------------- All the coordinates that had been available in NDB format are now also available in PDB format. These files are located in the directory called coord_pdb. To obtain a coordinate file in PDB format send the following mail message: To: ndblib@ndbserver.rutgers.edu Subject: send from coord_pdb where the word is replaced by the desired file name. The name of each file in this directory is the same as its NDB file name (NDB ID) with the .pdb extension added. For example, the PDB-format coordinate file for the structure bdl001 is called bdl001.pdb. For structures with only one strand per asymmetric unit, the coordinates for the complete double helix are available in a second file, with an 's' added to the file name. For example, structure adh008 has two PDB coordinate files: adh008.pdb and adh008.pdbs. For more information and a complete list of coordinate files available in this directory, please send the following mail message: To: ndblib@ndbserver.rutgers.edu Subject: send index from coord_pdb The PDB-format coordinate files can be accessed via anonymous ftp and gopher in the usual manner, by going to the directory coord_pdb. PERSONALIZED QUERIES: -------------------- Anyone who is interested in creating a report which is not found among the released ones can request a report by sending a message to the following e-mail address: To: ndbadmin@ndbserver.rutgers.edu We will create the report and send it back via electronic mail. NDB AVAILABLE VIA GOPHER: ------------------------ All the information on the NDB file server is now available via the Gopher service. The Internet Gopher is a distributed document delivery service which allows the user to access data from multiple hosts. The NDB gopher resides on host ndbgopher.rutgers.edu port 17105. On a character terminal based gopher, one would type the following command to connect to the NDB gopher server: gopher ndbgopher.rutgers.edu 17105 In addition, the NDB file server can also be accessed through the PDB Internet Gopher. On a terminal running X windows, one could type xgopher to run the X version of gopher. ACKNOWLEDGEMENTS: ---------------- The following article describing the Nucleic Acid Database project appeared in the September, 1992 issue of the Biophysical Journal: Helen M. Berman, Wilma K. Olson, David L. Beveridge, John Westbrook, Anke Gelbin, Tamas Demeny, Shu-Hsin Hsieh, A. R. Srinivasan, and Bohdan Schneider, 1992. The Nucleic Acid Database: A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J., 63, 751-759. Researchers who make use of information obtained from NDB, should use this citation. The Nucleic Acid Database Project represents a collaborative effort between Helen Berman and Wilma Olson of Rutgers University and David Beveridge of Wesleyan University, and is funded by the Division of Instrumentation and Resources of the National Science Foundation (BIR 90 12772).