10 20 30 40 50 60 70 80 2AWR - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER STRUCTURAL PROTEIN/DNA 02-SEP-05 2AWR
TITLE PROTAMINE-DNA COMPLEX 1
COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPERM PROTAMINE P1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYSTEINE-RICH PROTAMINE; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SPERM PROTAMINE P2; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: HISTONE P2, HP2, PROTAMINE P3, HP3, PROTAMINE P4, COMPND 9 HP4, BASIC NUCLEAR PROTEIN HPS1, BASIC NUCLEAR PROTEIN COMPND 10 HPS2, HPI1, HPI2; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 30-MER; COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: 30-MER; COMPND 17 CHAIN: D; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 5; COMPND 20 MOLECULE: 29-MER; COMPND 21 CHAIN: E, G; COMPND 22 ENGINEERED: YES; COMPND 23 MOL_ID: 6; COMPND 24 MOLECULE: 29-MER; COMPND 25 CHAIN: F, H; COMPND 26 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 6 ORGANISM_COMMON: HUMAN; SOURCE 7 MOL_ID: 3; SOURCE 8 SYNTHETIC: YES; SOURCE 9 MOL_ID: 4; SOURCE 10 SYNTHETIC: YES; SOURCE 11 MOL_ID: 5; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 6; 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 2AWR 1 JRNL REVDAT 1 27-SEP-05 2AWR 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 2AWR 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 RCSB034405.
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 THE STRUCTURE OF ONE COMPLETE "UNIT CELL" (SEE REMARK 220 THE FOLLOWING) OF THE PROTAMINE-DNA COMPLEX. THERE IS REMARK 220 ALSO A "MODEL OF THE MODEL", ENTITLED "PROTAMINE- DNA REMARK 220 COMPLEX 2", WHICH CONTAINS ONLY ARGININE RESIDUES, AND REMARK 220 IS ONLY 4 RESIDUES IN LENGTH. IT ILLUSTRATES THE REMARK 220 PRINCIPLES OF PROTAMINE-DNA IONIC BINDING FAR MORE REMARK 220 CLEARLY THAN THE COMPLETE STRUCTURE, WHICH IS LIKE REMARK 220 LOOKING INTO A FOREST. THE "MODEL OF THE MODEL" ALSO REMARK 220 ILLUSTRATES THE MANNER OF LATERAL ASSOCIATION OF REMARK 220 ADJACENT "UNIT CELLS" THROUGH MUTUAL INTERCALATION OF REMARK 220 BASE PAIRS, AND THROUGH A REPEATING PATTERN OF SQUARE- REMARK 220 SHAPED ARRAYS OF SALT BRIDGES. THE "UNIT CELL" OF REMARK 220 PROTAMINE-DNA STRUCTURE CONSISTS OF PROTAMINE P1 AND P2 REMARK 220 (CHAINS A AND B) AND AN IONICALLY- BOUND DNA DUPLEX ON REMARK 220 EITHER SIDE (CHAINS C-D AND G-H). THE ADDITIONAL DUPLEX REMARK 220 (CHAINS E-F) IS PART OF AN ADJACENT "UNIT CELL", AND IS REMARK 220 INCLUDED TO SHOW THE MANNER OF BINDING OF ADJACENT UNIT REMARK 220 CELLS BY MUTUAL INTERCALATION OF DNA BASES. 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 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AWS RELATED DB: PDB
DBREF 2AWR A 1 51 UNP P04553 HSP1_HUMAN 0 50 DBREF 2AWR B 1 57 UNP P04554 HSP2_HUMAN 46 102
SEQADV 2AWR GLY B 5 UNP P04554 GLN 50 CONFLICT
SEQRES 1 A 51 MET ALA ARG TYR ARG CYS CYS ARG SER GLN SER ARG SER SEQRES 2 A 51 ARG TYR TYR ARG GLN ARG GLN ARG SER ARG ARG ARG ARG SEQRES 3 A 51 ARG ARG SER CYS GLN THR ARG ARG ARG ALA MET ARG CYS SEQRES 4 A 51 CYS ARG PRO ARG TYR ARG PRO ARG CYS ARG ARG HIS SEQRES 1 B 57 ARG THR HIS GLY GLY SER HIS TYR ARG ARG ARG HIS CYS SEQRES 2 B 57 SER ARG ARG ARG LEU HIS ARG ILE HIS ARG ARG GLN HIS SEQRES 3 B 57 ARG SER CYS ARG ARG ARG LYS ARG ARG SER CYS ARG HIS SEQRES 4 B 57 ARG ARG ARG HIS ARG ARG GLY CYS ARG THR ARG LYS ARG SEQRES 5 B 57 THR CYS ARG ARG HIS SEQRES 1 C 30 G T A C G T A C G T A C G SEQRES 2 C 30 T A C G T A C G T A C G T SEQRES 3 C 30 A C G T SEQRES 1 D 30 A C G T A C G T A C G T A SEQRES 2 D 30 C G T A C G T A C G T A C SEQRES 3 D 30 G T A C SEQRES 1 E 29 G T A C G T A C G T A C G SEQRES 2 E 29 T A C G T A C G T A C G T SEQRES 3 E 29 A C G SEQRES 1 F 29 C G T A C G T A C G T A C SEQRES 2 F 29 G T A C G T A C G T A C G SEQRES 3 F 29 T A C SEQRES 1 G 29 G T A C G T A C G T A C G SEQRES 2 G 29 T A C G T A C G T A C G T SEQRES 3 G 29 A C G SEQRES 1 H 29 C G T A C G T A C G T A C SEQRES 2 H 29 G T A C G T A C G T A C G SEQRES 3 H 29 T A C
SHEET 1 A 2 ALA A 2 PRO A 42 0 SHEET 2 A 2 ARG B 9 THR B 49 1 O CYS B 13 N CYS A 6 SHEET 1 B 2 ARG A 49 ARG A 50 0 SHEET 2 B 2 ARG B 56 HIS B 57 1 O HIS B 57 N ARG A 49
SSBOND 1 CYS A 6 CYS B 13 SSBOND 2 CYS A 30 CYS B 37 SSBOND 3 CYS A 40 CYS B 47
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