MSOE Center for BioMolecular Modeling Plasma Membrane Kit | 1

Below is the collection of commands that will transform

the Protein Databank (PDB) file 1zaa.pdb into the

plaster 3D printed model you have received as part of

the MMW1 - 2014 summer workshop.

Restrict and Color Backbone: restrict 4-31 and :c

cartoon off spacefill off

wireframe off

backbone 1.5

select helix

color red

select 31

color red

select sheet

color yellow

Add Sidechains and Color Sidechains: select arg18 and (sidechain or alpha)

spacefill 1.25

wireframe 1.0

select phe16 and (sidechain or alpha)

spacefill 1.25

wireframe 1.0

select leu22 and (sidechain or alpha)

spacefill 1.25

wireframe 1.0

select his25 and (sidechain or alpha)

spacefill 1.25

Designing a Zinc Finger Based on 1zaa.pdb

MSOE Center for BioMolecular Modeling Plasma Membrane Kit | 2

wireframe 1.0

select his29 and (sidechain or alpha)

spacefill 1.25

wireframe 1.0

select cys7 and (sidechain or alpha)

spacefill 1.25

wireframe 1.0

select cys12 and (sidechain or alpha)

spacefill 1.25

wireframe 1.0

select sidechain

color cpk

Add Zinc Ion and Struts Select zn201

Spacefill 1.5

Color lightgreen

connect (({1158})) (({485})) Strut

connect (({1158})) (({519})) Strut

connect (({1158})) (({674})) Strut

connect (({1158})) (({637})) Strut

select all

strut 1.0

color strut white

www.pdb.orginfo@rcsb.org

About the RCSB PDB Molecule of the MonthUsing selected molecules from the PDB

archive, each feature includes an introduction to the structure and function ofthe molecule, a discussion of its relevance to

human health and welfare, and suggestions for viewing and

accessing further details.

The RCSB PDB Molecule of the Month is read by students, teachers, and scientists

worldwide at www.pdb.org.

This March 2007 edition was written and illustrated by David S. Goodsell

(RCSB PDB and The Scripps Research Institute).

MOLECULE OF THE MONTH:

ZINC FINGERS

Small and MightyOur cells, on the other hand, often use a zinc atomto take a short cut. By arranging two cysteines andtwo histidines close to each other in a chain, a pro-tein can grab a zinc ion and fold tightly around it.In these proteins, termed zinc fingers, a short chainof 20-30 amino acids is enough to create a solid,stable structure. Zinc fingers are so useful that theyare found in thousands of our proteins, and arecommon in all plants and animals. Surprisingly,however, bacteria do not appear to take advantageof these little structures.

Sticky FingersMany zinc fingers play essential roles in DNArecognition. Zinc fingers were originally discov-ered in the transcription factor TFIIIA from frogeggs, which contains nine zinc fingers in a row.The two structures shown here capture pieces ofthis protein performing its functions. PDB entry1tf6, shown on the left, includes 6 of the zincfingers (blue) bound to a long stretch of DNA(red). With this interaction, TFIIIA helps controlthe transcription of the gene for a ribosomal

RNA. As shown on the right, TFIIIA also bindsto the ribosomal RNA itself, as seen in the twoPDB entries 1un6 (pictured) and 2hgh. Thesestructures include 3 of the 9 zinc fingers (blue),along with a small piece of the ribosomal RNA(red). In the frog eggs, about 10 billion copies ofthis protein help to stabilize the many copies ofRNA as the cell develops.

Modular RecognitionAs you can see from these structures, the string ofzinc fingers curls along the DNA or RNAstrands, binding in the grooves and extendingamino acids inwards to read the bases. A singlezinc finger does not bind very tightly and canonly recognize 2 or 3 base pairs. But when sever-al are strung together, the group binds moretightly and can read longer DNA sequences. Thismodular approach is so appealing thatresearchers are currently trying to design artificialzinc fingers with different specificities. Then, bylinking them up in the proper order, we couldcreate a custom zinc finger protein to read anysequence that we desire.

As you are browsing through the proteins in thePDB, you may notice something: most proteins are

big. They contain hundreds of amino acids, eventhough most of the work is often done by a few

amino acids on one side. Why are proteins so big?One reason that proteins are so large is that they

must self-assemble inside cells. Proteins are built asfloppy chains that fold all by themselves (or with a

little help from chaperones) into stable, compactstructures. These folded structures are stabilized by

hydrogen bonds, charge-charge interactions andhydrophobic forces between the different amino

acids, which all line up like pieces in a jigsaw puzzlewhen the protein folds. A single hydrogen bond or a

few charge pairs would not be enough, but a chain ofhundreds of amino acids has hundreds of interactionsthat together glue the protein into a stable structure.

1tf6

1un6, 2hgh

RCSB Protein Data BankThe Protein Data Bank (PDB) is thesingle worldwide repository for the processing and distribution of 3D

structure data of large molecules ofproteins and nucleic acids. The RCSBPDB is operated by Rutgers, The StateUniversity of New Jersey and the SanDiego Supercomputer Center and the

Skaggs School of Pharmacy andPharmaceutical Sciences at the Universityof California, San Diego–two members

of the Research Collaboratory forStructural Bioinformatics (RCSB).

It is supported by funds from theNational Science Foundation, the

National Institute of General MedicalSciences, the Office of Science,

Department of Energy, the NationalLibrary of Medicine, the National

Cancer Institute, the National Instituteof Neurological Disorders and Strokeand the National Institute of Diabetes

& Digestive & Kidney Diseases.

The RCSB PDB is a member ofthe worldwide PDB

(wwPDB; www.wwpdb.org).

References: 1tf6: R. T. Nolte, R. M. Conlin, S. C. Harrison, R. S. Brown(1998) Differing roles for zinc fingers in DNA recognition:structure of a six-finger transcription factor IIIA complex.Proc.Natl.Acad.Sci.USA 95, 2938-2943.

1un6: D. Lu, M. A. Searles, A. Klug (2003) Crystalstructure of a zinc-finger-RNA complex reveals twomodes of molecular recognition. Nature 426, 96.

2hgh: B. M. Lee, J. Xu, B. K. Clarkson, M. A. Martinez-Yamout, J. H. Dyson, D. A. Case, J. M. Gottesfeld, P. E.Wright (2006) Induced fit and "lock and key" recogni-tion of 5S RNA by zinc fingers of transcription factorIIIA. J.Mol.Biol. 357, 275-291.

1y0j: C. K. Liew, R. J. Y. Simpson, A. H. Y. Kwan, L. A.Crofts, F. E. Loughlin, J. M. Matthews, M. Crossley, J. P.Mackay (2005) Zinc fingers as protein recognition motifs:structural basis for the GATA-1/friend of GATA interac-tion. Proc.Natl.Acad.Sci.Usa 102, 583-588.

1a1t: R. N. De Guzman, Z. R. Wu, C. C. Stalling, L.Pappalardo, P. N. Borer, M. F. Summers (1998) Structure ofthe HIV-1 nucleocapsid protein bound to the SL3 psi-RNArecognition element. Science 279, 384-388.

1joc: J. J. Dumas, E. Merithew, E. Sudharshan, D.Rajamani, S. Hayes, D. Lawe, D. Corvera, D. G.Lambright (2001) Multivalent endosome targeting byhomodimeric EEA1. Mol.Cell 8, 947-958.

1znf: M. S. Lee, G. P. Gippert, K. V. Soman, D. A. Case,P. E. Wright (1989) Three-dimensional solution structureof a single zinc finger DNA-binding domain. Science245, 635-637.

1zaa: N. P. Pavletich, C. O. Pabo (1991) Zinc finger-DNA recognition: crystal structure of a Zif268-DNAcomplex at 2.1 A. Science 252, 809-817.

S. A. Wolfe, L. Nekludova and C. O. Pabo (1999) DNArecognition by Cys2His2 zinc finger proteins. AnnualReview of Biophysics and Biomolecular Structure 3,183-212.

J. H. Laity, B. M. Lee and P. E. Wright (2001) Zinc fingerproteins: new insights into structural and functional diversi-ty. Current Opinion in Structural Biology 11, 39-46.

J. M. Matthews and M. Sunde (2002) Zinc fingers--foldsfor many occasions. IUBMB Life 54, 351-355.

S. S. Krishna, I. Majumdar and N. V. Grishin (2003)Structural classification of zinc fingers. Nucleic AcidsResearch 31, 532-550.

R. Gamsjaeger, C. K. Liew, F. E. Loughlin, M. Crossleyand J. P. Mackay (2007) Sticky fingers: zinc fingers asprotein-recognition motifs. Trends in Biochemical Sciences32, 63-70.

ZINC FINGERS

Exploring the StructureWhen you go to the PDB to explore zinc fingers, trynot to be overwhelmed: there are currently over athousand structures containing all sorts of zinc fin-gers, knuckles, treble clefs, ribbons, and other fanci-ful folds. The structure shown on the left, from PDBentry 1znf, shows a classic zinc finger. Since it's sucha small structure, with only 25 amino acids, it'sworth taking a closer look at what each part is doing.The two cysteines and two histidines are shown atthe bottom, arranged in a tetrahedron around thezinc. Just above them, a phenylalanine and a leucine

form a tiny hydrophobic core inside the small fold-ed chain. The rest of the amino acids all face more-or-less outwards, and can be used for various func-tional tasks. For DNA binding proteins, the aminoacids at the top of the alpha helix are typically usedfor recognition. This is shown on the structure atright, from PDB entry 1zaa. It contains three linkedzinc fingers bound to DNA. The amino acids shownin red extend towards the DNA and read the basesequence, as shown in the lower figure where theDNA is removed.

These pictures were created with RasMol.

Jack of All TradesZinc fingers come in many shapes and sizes, butthey all have one or more zinc atoms (shown herein green) gripped by a combination of four aminoacids, either cysteine or histidine (shown on thepicture on the bottom of the page). Zinc fingersperform many different jobs, as shown in thesethree sample structures. The complex at upper left(PDB entry 1y0j) shows zinc fingers from twolonger proteins, GATA-1 (which contains two zincfingers) and FOG-1 (which contains 9 zinc fin-gers). The specific interaction between these twozinc fingers plays an essential role in the develop-ment of blood cells. The HIV-1 nucleocapsid pro-tein shown at lower left (PDB entry 1a1t) containstwo zinc fingers that grip the viral RNA duringbudding of the virus. The protein EEA1, shown atthe right from PDB entry 1joc, contains two zincfingers in each chain. It binds to a special lipid foundin endosomes, and plays an essential role in trans-porting molecules to that cellular compartment.

1y0j

1a1t

1znf

1zaa

1joc