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protein dna_rna Protein-protein interface(s) links
Transcription/DNA PDB id
3cro
Jmol
Contents
Protein chains
66 a.a. *
DNA/RNA
Waters ×25
* Residue conservation analysis
PDB id:
3cro
Name: Transcription/DNA
Title: The phage 434 cro/or1 complex at 2.5 angstroms resolution
Structure: DNA (5'- d( Ap Ap Gp Tp Ap Cp Ap Ap Ap Cp Tp Tp Tp Cp Tp Tp G p Tp Ap T)-3'). Chain: a. Engineered: yes. DNA (5'- d( Tp Ap Tp Ap Cp Ap Ap Gp Ap Ap Ap Gp Tp Tp Tp Gp T p Ap Cp T)-3'). Chain: b.
Source: Synthetic: yes. Phage 434. Organism_taxid: 10712
Biol. unit: Tetramer (from PQS)
Resolution:
2.50Å     R-factor:   0.220    
Authors: A.Mondragon,S.C.Harrison
Key ref: A.Mondragón and S.C.Harrison (1991). The phage 434 Cro/OR1 complex at 2.5 A resolution. J Mol Biol, 219, 321-334. PubMed id: 2038059 DOI: 10.1016/0022-2836(91)90568-Q
Date:
06-Jul-90     Release date:   15-Oct-91    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P03036  (RCRO_BP434) -  Regulatory protein cro
Seq:
Struc: 		71 a.a.
66 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of transcription   3 terms 
  Biochemical function     DNA binding     3 terms  

 

 
DOI no: 10.1016/0022-2836(91)90568-Q J Mol Biol 219:321-334 (1991)
PubMed id: 2038059  
 
 
The phage 434 Cro/OR1 complex at 2.5 A resolution.
A.Mondragón, S.C.Harrison.
 
  ABSTRACT  
 
The crystal structure of phage 434 Cro protein in complex with a 20 base-pair DNA fragment has been determined to 2.5 A resolution. The DNA fragment contains the sequence of the OR1 operator site. The structure shows a bent conformation for the DNA, straighter at the center and more bent at the ends. The central base-pairs adopt conformations with significant deviations from coplanarity. The two molecules interact extensively along their common interface, both through hydrogen bonds and van der Waals interactions. The significance of these interactions for operator binding and recognition is discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
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Pushing the limits of what is achievable in protein-DNA docking: benchmarking HADDOCK's performance.
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19019826 S.Russo, J.E.Schweitzer, T.Polen, M.Bott, and E.Pohl (2009).
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PDB codes: 3f51 3f52
17652321 K.Yamasaki, T.Akiba, T.Yamasaki, and K.Harata (2007).
Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1.
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PDB codes: 2o49 2o4a
17855396 S.H.Chan, Y.Bao, E.Ciszak, S.Laget, and S.Y.Xu (2007).
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16820531 M.van Dijk, A.D.van Dijk, V.Hsu, R.Boelens, and A.M.Bonvin (2006).
Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility.
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14627811 C.Laguri, M.K.Phillips-Jones, and M.P.Williamson (2003).
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12511493 K.Fromknecht, P.D.Vogel, and J.G.Wise (2003).
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12598646 K.R.LeFevre, and M.H.Cordes (2003).
Retroevolution of lambda Cro toward a stable monomer.
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10888200 F.A.Etzkorn, and J.M.Travins (2000).
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Crystal structure of the N-terminal domain of the DnaB hexameric helicase.
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10570130 O.Littlefield, Y.Korkhin, and P.B.Sigler (1999).
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9635768 I.Rouzina, and V.A.Bloomfield (1998).
DNA bending by small, mobile multivalent cations.
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9518483 R.E.Dickerson (1998).
DNA bending: the prevalence of kinkiness and the virtues of normality.
  Nucleic Acids Res, 26, 1906-1926.  
  9023183 J.S.Hwang, J.Yang, and A.J.Pittard (1997).
Critical base pairs and amino acid residues for protein-DNA interaction between the TyrR protein and tyrP operator of Escherichia coli.
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  9032054 M.A.Kercher, P.Lu, and M.Lewis (1997).
Lac repressor-operator complex.
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  J Biol Chem, 272, 17966-17971.  
9396800 N.M.Luscombe, R.A.Laskowski, and J.M.Thornton (1997).
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9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
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8790361 D.A.Liberles, and P.B.Dervan (1996).
Design of artificial sequence-specific DNA bending ligands.
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8798534 F.Pio, R.Kodandapani, C.Z.Ni, W.Shepard, M.Klemsz, S.R.McKercher, R.A.Maki, and K.R.Ely (1996).
New insights on DNA recognition by ets proteins from the crystal structure of the PU.1 ETS domain-DNA complex.
  J Biol Chem, 271, 23329-23337.  
8880931 H.Wako, M.Tachikawa, and A.Ogawa (1996).
A comparative study of dynamic structures between phage 434 Cro and repressor proteins by normal mode analysis.
  Proteins, 26, 72-80.  
8924205 J.A.Bousquet, and N.Ettner (1996).
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  7709431 C.W.Sokolik (1995).
Kinemages: make your own molecules for teaching.
  Trends Biochem Sci, 20, 122-124.  
7716167 J.Janin (1995).
Elusive affinities.
  Proteins, 21, 30-39.  
7647248 M.A.Young, G.Ravishanker, D.L.Beveridge, and H.M.Berman (1995).
Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes.
  Biophys J, 68, 2454-2468.  
8749848 M.Suzuki, and M.Gerstein (1995).
Binding geometry of alpha-helices that recognize DNA.
  Proteins, 23, 525-535.  
7610037 M.Suzuki, and N.Yagi (1995).
Stereochemical basis of DNA bending by transcription factors.
  Nucleic Acids Res, 23, 2083-2091.  
  8590003 T.E.Strzelecka, G.M.Clore, and A.M.Gronenborn (1995).
The solution structure of the Mu Ner protein reveals a helix-turn-helix DNA recognition motif.
  Structure, 3, 1087-1095.
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8075315 A.E.Garcia, D.M.Soumpasis, and T.M.Jovin (1994).
Dynamics and relative stabilities of parallel- and antiparallel-stranded DNA duplexes.
  Biophys J, 66, 1742-1755.  
8161709 E.Stofer, and R.Lavery (1994).
Measuring the geometry of DNA grooves.
  Biopolymers, 34, 337-346.  
  8156594 J.D.Klemm, M.A.Rould, R.Aurora, W.Herr, and C.O.Pabo (1994).
Crystal structure of the Oct-1 POU domain bound to an octamer site: DNA recognition with tethered DNA-binding modules.
  Cell, 77, 21-32.
PDB code: 1oct
7971994 M.S.Finnin, D.W.Hoffman, and S.W.White (1994).
The DNA-binding domain of the MotA transcription factor from bacteriophage T4 shows structural similarity to the TATA-binding protein.
  Proc Natl Acad Sci U S A, 91, 10972-10976.  
7809040 M.Suzuki, and N.Yagi (1994).
DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families.
  Proc Natl Acad Sci U S A, 91, 12357-12361.  
  8087558 M.Suzuki (1994).
A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules.
  Structure, 2, 317-326.  
8332454 B.E.Withers, and J.C.Dunbar (1993).
The endonuclease isoschizomers, SmaI and XmaI, bend DNA in opposite orientations.
  Nucleic Acids Res, 21, 2571-2577.  
8233830 D.J.Kessler, B.M.Pettitt, Y.K.Cheng, S.R.Smith, K.Jayaraman, H.M.Vu, and M.E.Hogan (1993).
Triple helix formation at distant sites: hybrid oligonucleotides containing a polymeric linker.
  Nucleic Acids Res, 21, 4810-4815.  
  8081737 D.W.Rodgers, and S.C.Harrison (1993).
The complex between phage 434 repressor DNA-binding domain and operator site OR3: structural differences between consensus and non-consensus half-sites.
  Structure, 1, 227-240.
PDB code: 1per
  8449883 J.Yang, S.Ganesan, J.Sarsero, and A.J.Pittard (1993).
A genetic analysis of various functions of the TyrR protein of Escherichia coli.
  J Bacteriol, 175, 1767-1776.  
1518844 Y.Takeda, P.D.Ross, and C.P.Mudd (1992).
Thermodynamics of Cro protein-DNA interactions.
  Proc Natl Acad Sci U S A, 89, 8180-8184.  
  1682054 C.Wolberger, A.K.Vershon, B.Liu, A.D.Johnson, and C.O.Pabo (1991).
Crystal structure of a MAT alpha 2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions.
  Cell, 67, 517-528.
PDB code: 1apl
1870967 G.B.Koudelka (1991).
Bending of synthetic bacteriophage 434 operators by bacteriophage 434 proteins.
  Nucleic Acids Res, 19, 4115-4119.  
1923807 J.A.Shin, R.H.Ebright, and P.B.Dervan (1991).
Orientation of the Lac repressor DNA binding domain in complex with the left lac operator half site characterized by affinity cleaving.
  Nucleic Acids Res, 19, 5233-5236.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.