Table 6.

DNA‐Binding Proteins

Protein	PDB entrya	Reference
Helix‐Turn‐Helix Motifs
Prokaryotic and phage repressors
λ Cro protein	1cro	Anderson et al. (1981)
λ‐repressor	1lmb	Jordan and Pabo (1988)
434 repressor	2or1	Aggarwal et al. (1988)
434 cro protein	2cro	Wolberger et al. (1988)
Homeodomains or homeodomain‐like
Engrailed	1hdd	Kissinger et al. (1990)
Antennapedia	1hom	Qian et al. (1989)
Oct‐1 POU	1oct	Klemm et al. (1994)
Proto onco gene product Myb	1mse	Ogata et al. (1994)
Hin‐related prokaryotic DNA recombinase	1hcr	Feng et al. (1994)
Winged helix
HNF‐3/fork head transcription factor	2hfh	Clark et al. (1993), Marsden et al. (1998)
Globular domain of histone H5	1hst	Ramakrishnan et al. (1993)
ETS transcription factor	1etc	Donaldson et al. (1996)
E. coli CAP protein	1cgp	Schultz et al. (1991)
Biotin repressor	1bia	Wilson et al. (1992)
PurR repressor
PurR repressor	1pru	Schumacher et al. (1994)
Zinc‐containing DNA‐binding motifs
Cys 2 His 2 zinc fingers
ZIF286	1zaa	Pavletich and Pabo (1991)
GLI oncogene product	2gli	Pavletich and Pabo (1993)
Tramtrack	2drp	Fairall et al. (1993)
Zinc ribbon motif
Transcription elongation factor TFIIS	1tfi	Qian et al. (1993)
Transcription initiation factor TFIIB	1pft	Zhu et al. (1996)
RNA Polymerase II RPB9 fragment	1qyp	Wang et al. (1998)
DNA primase fragment	1d0q	Pan and Wigley (2000)
GATA‐binding motif
GATA‐1	1gat	Omichinski et al. (1993)
Zn2Cys6 binuclear cluster
GAL‐4	1d66	Marmorstein et al. (1992)
Pyrimidine pathway regulator 1(PPR1)	1pyi	Marmorstein and Harrison (1994)
PUT3	1zme	Swaminathan et al. (1997)
CD2‐LAC9	1cld	Gardner et al. (1995)
Nuclear hormone receptor DNA‐binding domains
Glucocorticoid receptor	1gdc	Luisi et al. (1991)
Estrogen receptor	1hcq	Schwabe et al. (1993)
Orphan nuclear receptor NGFI‐B	1cit	Meinke and Sigler (1999)
Thyroid hormone receptor	2nll	Rastinejad et al. (1995)
MADS box domain
Serum response factor	1srs	Pellegrini et al. (1995)
MCM1 transcriptional regulator	1mnm	Tan and Richmond (1998)
MEF2A core	1egw	Santelli and Richmond (2000)
Basic leucine zipper
GCN4 homodimer	1ysa	Ellenberger et al. (1992)
c‐Fos:c‐Jun heterodimer	1fcs	Glover and Harrison (1995)
Helix‐loop‐helix
MAX transcription factor	2an2	Ferre‐D'Amare et al. (1993)
MyoD transcription activator	1mdy	Ma et al. (1994)
Upstream stimulatory factor	1an4	Ferre‐D'Amare et al. (1994)
Transcription factor E47	—	Ellenberger et al. (1994)
HMG box domain
Human SRY	1hry	Werner et al. (1995)
LEF‐1 transcription factor	1lef	Love et al. (1995)
HMG1 B domain	1hme	Weir et al. (1993)
Histone‐fold proteins
Nucleosomal core octamer (H2A, H2B, H3, H4)	1hio	Arents et al. (1991)
Drosophila TAFII42 and TAFII62	1taf	Xie et al. (1996)
Human TAFII28 and TAFII18	1bh9	Birck et al. (1998)
Negative cofactor 2	1jfi	Kamada et al. (2001)
HMFA and HMFB Archeon histones	1b67	Decanniere et al. (2000)
β‐sheet motifs
Ribbon‐helix‐helix
Arc repressor	1par	Raumann et al. (1994)
Met repressorb	1cma	Somers and Phillips (1992)
Mnt repressor	1mnt	Burgering et al. (1994)
Histone‐like HU family
Histone‐like protein (HU)	1hue	Tanaka et al. (1984), Vis et al. (1995)
Integration host factor (IHF)/DNA complex	1ihf	Rice et al. (1996)
DNA‐binding protein TF1	1wtu	Jia et al. (1996)
TBP family
TATA box–binding protein/DNA complex	1ytb/1tgh	Kim et al. (1993a,b)
Ig‐like transcription factors
p53 tumor supressors
Human p53/DNA complex	1tsr, 1tup	Cho et al. (1994)
Mouse p53 DNA‐binding domain	1hu8	Zhao et al. (2001)
NF‐κB
p50/p50/DNA complex	1nfk, 1svc	Ghosh et al. (1995), Muller et al. (1995)
p52/p52/DNA complex	1a3q	Cramer et al. (1997)
p65/p65/DNA complex	1ram	Chen et al. (1998d)
p65/p50/DNA complex	1vkx	Chen et al. (1998a)
NFAT
NFAT1/Fos/Jun/DNA complex	1a02	Chen et al. (1998b)
NFATC1/DNA complex	1a66	Zhou et al. (1998)
TonEBP/DNA complex	1imh	Stroud et al. (2002)
CBF
Human PEBP2(CBFα) runt domain	1cmo	Nagata et al. (1999)
Human CBFα runt domain	1co1	Berardi et al. (1999)
Human Runx‐1(CBFα)/CBFβ/DNA complex	1h9d	Bravo et al. (2001)
Mouse Runx‐1(CBFα)/CBFβ/DNA	1hjb	Tahirov et al. (2001)
Mouse Runx‐1(CBFα)/CBFβ/c‐EBPβ/DNA	1io4	Tahirov et al. (2001)
T‐domain
Xenopus laevis Brachyuri T‐domain/DNA complex	1xbr	Muller and Herrmann (1997)
Human TBX3 T‐domain/DNA complex	1h6f	Coll et al. (2002)
STAT proteins
STAT‐1/STAT‐1/DNA complex	1bf5	Chen et al. (1998c)
STAT3β/STAT3β/DNA complex	1bg1	Becker et al. (1998)

^aSee Web‐Based Structural Bioinformatics and http://www.rcsb.org/pdb. For proteins with no entry listed, coodinates have not been deposited in the Protein Data Bank.

^bThis protein is also known as MetJ.

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