HEADER STRUCTURAL PROTEIN/DNA 02-SEP-05 2AWS TITLE PROTAMINE-DNA COMPLEX 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPEAT PEPTIDE; COMPND 3 CHAIN: A, B, G, H, Q, R, W, X; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(P*GP*TP*A)-3'; COMPND 7 CHAIN: C, E, I, O, U; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(P*TP*AP*C)-3'; COMPND 11 CHAIN: D, F, J, T; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: 5'-D(P*GP*T)-3'; COMPND 15 CHAIN: K; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 5; COMPND 18 MOLECULE: 5'-D(P*AP*C)-3'; COMPND 19 CHAIN: L; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 6; COMPND 22 MOLECULE: 5'-D(P*GP*TP*AP*C)-3'; COMPND 23 CHAIN: M, N, S; COMPND 24 ENGINEERED: YES; COMPND 25 MOL_ID: 7; COMPND 26 MOLECULE: 5'-D(P*TP*AP*CP*G)-3'; COMPND 27 CHAIN: P, V; COMPND 28 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES; SOURCE 7 MOL_ID: 4; SOURCE 8 SYNTHETIC: YES; SOURCE 9 MOL_ID: 5; SOURCE 10 SYNTHETIC: YES; SOURCE 11 MOL_ID: 6; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 7; SOURCE 14 SYNTHETIC: YES KEYWDS DNA,HELIX,NON-HELICAL,TOPOLOGY,TOPOLOGICAL,TOPOLOGICALLY- KEYWDS 2 LINKED, TOPOLOGICALLY NON-LINKED,SIDE-BY-SIDE,STRAIGHT KEYWDS 3 LADDER,TERTIARY STRUCTURE EXPDTA THEORETICAL MODEL AUTHOR K.BIEGELEISEN REVDAT 2 01-AUG-06 2AWS 1 JRNL REVDAT 1 04-OCT-05 2AWS 0 JRNL AUTH K.BIEGELEISEN JRNL TITL THE PROBABLE STRUCTURE OF THE PROTAMINE-DNA JRNL TITL 2 COMPLEX. JRNL REF J.THEOR.BIOL. V. 241 533 2006 JRNL REFN ASTM JTBIAP UK ISSN 0022-5193 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2AWS COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-2005. REMARK 100 THE RCSB ID CODE IS RCSB034406. REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: THIS IS A PARTIAL STRUCTURE WHICH SHOWS THE MANNER OF REMARK 220 ASSOCIATION BETWEEN MULTIPLE "UNIT CELLS" (SEE THE REMARK 220 FOLLOWING). THE UNIT CELLS IN THIS FILE ARE LIMITED TO 4 REMARK 220 RESIDUES IN LENGTH. IF THE ENTIRETY OF EACH CHAIN WAS REMARK 220 REPRESENTED HERE, THE FILE WOULD BE PONDEROUS AND REMARK 220 UNWIELDY. THERE IS ANOTHER MODEL ON DEPOSIT, ENTITLED " REMARK 220 PROTAMINE-DNA COMPLEX 1", WHICH SHOWS THE ENTIRETY OF A REMARK 220 SINGLE UNIT CELL. THIS MODEL SHOWS CHAINS OF ONLY 4 REMARK 220 RESIDUES IN LENGTH, AND INCLUDES ONLY ARGININE RESIDUES. REMARK 220 IT SERVES TWO PURPOSES: (1) IT DEMONSTRATES THE REMARK 220 PRINCIPLES OF IONIC BONDING, BETWEEN THE POSITIVELY- REMARK 220 CHARGED GUANIDINIUM GROUPS OF ARGININE AND THE REMARK 220 NEGATIVELY-CHARGED PHOSPHATE GROUPS OF DNA, BETTER THAN REMARK 220 THE COMPLETE MODEL, WHERE LOOKING FOR THESE IONIC BONDS REMARK 220 IS LIKE LOOKING FOR A TREE IN A FOREST, AND (2) REMARK 220 ILLUSTRATES THE MANNER OF ASSOCIATION OF ADJACENT "UNIT REMARK 220 CELLS" (SEE THE FOLLOWING) THROUGH MUTUAL INTERCALATION REMARK 220 OF BASE PAIRS, AND THROUGH SALT BRIDGES. THE "UNIT CELL" REMARK 220 OF PROTAMINE-DNA STRUCTURE CONSISTS OF PROTAMINE P1 AND REMARK 220 P2 (FOR EXAMPLE, CHAINS G AND H) PLUS AN IONICALLY-BOUND REMARK 220 DNA DUPLEX ON EITHER SIDE (FOR EXAMPLE, CHAINS E-F AND I REMARK 220 -J). IN THE Y-AXIS DIRECTION THE UNIT CELLS BIND TO ONE REMARK 220 ANOTHER BY MUTUAL INTERCALATION OF DNA BASE PAIRS (FOR REMARK 220 EXAMPLE, C-D MUTUALLY INTERCALATING WITH E-F). REMARK 220 LATERALLY, THAT IS IN THE X-AXIS DIRECTION, THE UNIT REMARK 220 CELLS FORM A REPEATING PATTERN OF SQUARE ARRAYS OF SALT REMARK 220 BRIDGES, EACH CONSISTING OF TWO POSITIVELY-CHARGED REMARK 220 ARGININE GUANIDINIUM GROUPS ARRANGED DIAGONALLY, AND TWO REMARK 220 NEGATIVELY-CHARGED DNA PHOSPHATE GROUPS ALSO ARRANGED REMARK 220 DIAGONALLY. THESE SQUARE ARRAYS MAY BE IDENTIFIED BY THE REMARK 220 CHAIN IDENTIFIERS OF THE CHAINS CONSTITUTING THE CORNERS REMARK 220 OF THE SQUARES: BPQD, EQSH AND HVWJ. ALTHOUGH THE REMARK 220 STRUCTURES OF DNA AND PROTAMINE ARE INDIVIDUALLY KNOWN, REMARK 220 NO ONE HAS BEEN ABLE TO EVEN SUGGEST, MUCH LESS PROVE A REMARK 220 STRUCTURE FOR THE COMPLEX. A HELICAL STRUCTURE FOR THE REMARK 220 DNA IN THE COMPLEX CAN BE CONCLUSIVELY EXCLUDED FROM REMARK 220 LOGICAL CONSIDERATIONS ALONE. ONCE THE POSSIBILITY OF REMARK 220 NON-HELICAL DNA IS ACKNOWLEDGED, THE SOLUTION TO THE REMARK 220 PROBLEM BECOMES APPARENT. THIS MODEL IS THE ONLY REMARK 220 LOGICALLY-PLAUSABLE SOLUTION. MANY DETAILS OF THE MODEL, REMARK 220 SUCH AS THE RESIDUE SPACING, ARE TENTATIVE, BUT ITS REMARK 220 GENERAL FEATURES CANNOT BE AVOIDED, BECAUSE THERE IS NO REMARK 220 OTHER WAY TO ALIGN THE POSITIVE CHARGES ON PROTAMINE REMARK 220 WITH THE NEGATIVE CHARGES ON DNA. REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AWR RELATED DB: PDB REMARK 900 PROTAMINE-DNA COMPLEX 1 SEQRES 1 A 4 ARG ARG ARG ARG SEQRES 1 B 4 ARG ARG ARG ARG SEQRES 1 G 4 ARG ARG ARG ARG SEQRES 1 H 4 ARG ARG ARG ARG SEQRES 1 Q 4 ARG ARG ARG ARG SEQRES 1 R 4 ARG ARG ARG ARG SEQRES 1 W 4 ARG ARG ARG ARG SEQRES 1 X 4 ARG ARG ARG ARG SEQRES 1 C 3 G T A SEQRES 1 D 3 T A C SEQRES 1 E 3 G T A SEQRES 1 F 3 T A C SEQRES 1 I 3 G T A SEQRES 1 J 3 T A C SEQRES 1 K 2 G T SEQRES 1 L 2 A C SEQRES 1 M 4 G T A C SEQRES 1 N 4 G T A C SEQRES 1 O 3 G T A SEQRES 1 P 4 T A C G SEQRES 1 S 4 G T A C SEQRES 1 T 3 T A C SEQRES 1 U 3 G T A SEQRES 1 V 4 T A C G SHEET 1 A 2 ARG A 2 ARG A 3 0 SHEET 2 A 2 ARG B 2 ARG B 3 1 O ARG B 3 N ARG A 2 SHEET 1 B 2 ARG G 2 ARG G 3 0 SHEET 2 B 2 ARG H 2 ARG H 3 1 O ARG H 3 N ARG G 2 SHEET 1 C 2 ARG Q 2 ARG Q 3 0 SHEET 2 C 2 ARG R 2 ARG R 3 1 O ARG R 3 N ARG Q 2 SHEET 1 D 2 ARG W 2 ARG W 3 0 SHEET 2 D 2 ARG X 2 ARG X 3 1 O ARG X 3 N ARG W 2 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 MASTER 76 0 0 0 8 0 0 6 0 0 0 24 END