Biochemistry and Molecular Biology Program
Supported by HHMI awards to Kenyon College

Biomolecules at Kenyon
Molecular Biology Tutorials
using Jmol

by students from BIOL 263: Molecular Biology and Genomics

C. elegans Tc3 Transposase HTH DNA-binding Motif
van Pouderoyen et al, 1997, Protein Data Bank
Please advise Wade Powell of any corrections.

Jmola Java applet, is used to display these tutorials. (Note: Older chime-based tutorials are archived here.)

  • Jmol is a Javascript-based molecular visualization tool.
  • The above molecule, as well as all tutorials from 2012 onwards, use a new version of Jmol called JSmol which does not require Java.  These tutorials may take a few seconds to load when first run and may not run on older versions of browsers.  The JSmol tutorials are best viewed with the latest version of Google Chrome.
  • Make your own Jmol tutorials: Download model (works in JSmol v13) and instructions.
  • Further help on buttons: Jmol Sampler, Silva & Marcey, CLU

These tutorials were created by students in collaboration with faculty at Kenyon. Jmol was used to illustrate structural and chemical features of macromolecules. The pdb files were downloaded from the Protein Data Bank of the Research Collaboratory for Structural Bioinformatics.   For each tutorial, the authors listed maintain copyright.

Optional stereo viewing instructions here.  We recommend the Pokescope viewer. Request help here.

Jmol Tutorials Edited by Daniel Barich '05


Mtr4 RNA Helicase
Elizabeth Abrash '17 and Ulises Arbelo '16
Sonic Hedgehog Protein (SHH)
Keith Adler '17 Morgan Miller '18
Estradiol and the Estrogen Receptor
Ifeoma Archimalo '18 and Sarah Kazzaz '18
Human Tryptophanyl-tRNA Synthetase Recognition and Specificity
Christiana Binkley '17 and Grace Riley '18
Retinoblastoma Binding Protein
Geoff Carney-Knisely '18 and Liz Eder '17
Glycogen Synthase Kinase-3beta (GSK-3beta)
Ren DeBrosse '18 and Katie Kaestner '16
Scott H. Freeburg '16 and Rachel Schafer '18
Wild Type Core Streptavidin
Nicholas Gutsche '17 and Jack Clayton '17
Human Salivary Amylase
Alexandra Simic Hachmann '17 and Daniel Maffezzoli '17
µ-opioid Receptor
Taylor Jamil '17 and Eliana McCann Smith '17
Streptococcus pyogenes CRISPR-Cas9 in Complex with Guide RNA and DNA
Trevor Manz '17 and Laura Duncan '17
Insulin Interactions with the Insulin Receptor
Taylor Maurer '17 and Morgan Perrett '17
S. cerevisiae Topoisomerase II-DNA-AMPPNP Complex
Jonathan Pang '17 and Kenyatta Viel '17
E. coli Restriction Endonuclease
Caitlin Redak '17 and Ambert Sawaya '17
Oligosaccharride Flippase in C.jejuni
Alex Schaal and Toby SantaMaria
H. sapiens Caspase-3
Alex Seaver '17 and Coire Gavin-Hanner '18
Dronpa: A Photoswitchable Protein Derived from Coral (Pectiniidae)
Maria Sorkin '16 and Emily Bulik-Sullivan '16
Inhibitor Tagetitoxin in Complex with T.Thermophilus RNA Polymerase
Faiza Sulaiman '15 and Kalkidan Aseged '17


Tryptophan Regulated Attenuation Protein (TRAP)
 Caroline Burley '17 and Natalie Plick '16
M. musculus Circadian Rhythm Protein CLOCK:BMAL1
Spencer Byers '16 and Kyle Hardacker '15
H. sapiens Exoribonuclease of viral RNA
  Blake Calcei '16, Brandon January '15 and Alexander McQuiston '16
RNA Polymerase II with Transcription Factor IIB
Jason Cinti ('16) and Issam Hamdallah ('16)
Zaire Ebola VP35 Protein
Kye Duren '16 and Rhea Le '16

S. lividans pH-Gated Potassium Channel
Hardy Evans '15 and Kevin Pan '15
Human Topoisomerase I and DNA Complex
Nat Fox '16 and Yohanna Ewing '16
S. cerevisiae DNA binding protein RAP-1
  Mattias Galliano '15 and Tomas Grant '16
Solanum lycopersicum ACC Synthase
Amanda He '16 and Andrew Pearlman '15
Kasugamycin Function in Thermus thermophilus 30S Ribosomal Subunit: Inhibition of Canonical Translation
Edna Kemboi '16 and Jiayu Chen '17
The Exon Junction Complex
Charlotte Leblang '16 and Daniel Jurgens '16
E. coli Aspartate Transcarbamoylase (ATCase)
Sanderlin '15 and Kaitlin Creamer '16
HIV Viral Infectivity Factor BC-box in complex with ElonginB and ElonginC
David Torres '16 and Joey Duronio '16


Serotonin (5-HT1B) Receptor Bound to Ergotaminerchaeal
Jourdan Cline '15 and Johanna Klinman '15
Rhodopsin GPCR
Katharina Devitofranceschi '14 Noah Winters '15
Homo sapiens Tyrosine Kinase Domain of Fibroblast Growth Factor Receptor 1
Luke Kresslein '15 and Lillian Spetrino '15
Telomerase Catalytic Subunit TERT in Tribolium castaneum
Shirley Lu '15 and Nicole Valentini '14
Activation and Regulation of Human Mitochondrial Transcription Factor A
 Kelsey McMurtry '14 and Wesley Manz '15
H. sapiens Transcriptional Coactivator p300/CREB-Binding Protein Associating Factor (PCAF)
Camelia Milnes '15 and Shannon Wright '16
Uracil-DNA Glycosylase
  Rei Mitsuyama '15 and Holden Richards '15
Human FEN1-PCNA Complex
  Maria Narvaez '14 and Hailey Schneider '14
Domain 2 of the Saccharomyces cerevisiae DEAD-Box Helicase Mss116p
Cristina Nunes '15 and Robert Turlington '16
Epstein-Barr Virus ZEBRA Protein DNA Binding Domain
Alexander Oles '16 and Stephanie Penix '16
 Human DNA Ligase IV-Artemis Fragment Complex
 Sean Smith '16 and Samantha White '16
Homo Sapiens Transforming Growth Factor, Beta-III
Jonathan Sun '16 and Stephanie Cordonnier '15


Dihydropteroate Synthase
Lyra Hall '14 and Rina Petek '15
Iron Regulatory Protein 1 in Complex with Ferritin IRE-mRNA: the Moonlighting Form of c-Aconitase
Michael Harden '14 and Marta Hamilton '14
Homo sapien Liver X Receptor Beta Kelly Heilman '12 and Crystal Piras '12
Oligoduplex Structure and Dimethylated DNA Base-Flipping Activity of the N-terminal Domain of E. coli Endonuclease McrB
Maggie Koenecke '15 and Eric Engelbrecht '14

Homodimeric Structure and DNA-Binding Activity of the Tyrosine Phosphorylated STAT-1 Dimer
Ainsley Lockhart '13 and Kendra Lechtenberg '13
Crystal Structure of the Beta-2 Adrenergic Receptor-Gs Protien Complex
Andrew Maurer '14 and Sam McQuiston '14
Binding Pocket Specificity and Key Amino Acids
Zach Morrow '14 and Kotiba Malek '14
Human Pancreatic RNase 1 in Complex with the Human Ribonuclease Inhibitor Protein
Mithzy Pena '14 and Haley Dugan '14
Structure of Estrogen Related Receptor Gamma in complex with Bisphenol A
 Ian Richardson and Myles Alderman
Ultraviolet Damage Endonuclease
Q Tashiro '15 and Rachel Rhee '15
Human Argonaute 2
Scott Watters '14 and Stephen Raithel '13


Oct and Sox POU/HMG/DNA complex Ariel Bartholomew '13 and Kate Haller '13
Staphylococcus aureus PBP4 in complex with ampicillin Joshua Bloom '13 and Kushal Rao '13
Prototype Foamy Virus (PFV) Intasome Clara Fischman '13 and Katie Adlam '13
Homo sapiens Liver X Receptor Beta Kelly Heilman '12 and Crystal Piras '12
UCHL3 in Plasmodium falciparum Morgan Korinek '12 and Andrea Pohly '12
Structure and Function of DNA Methyltransferase 1 Willie Miller-Little & Austin Griffin
Selenoenzyme Glutathione Peroxidase Sam Pletz '13 and Jimmy Chapman '13
Tetrameric Structure of IRF-3 with DNA Andy Schwartz '12 and Luke Sullivan '12
Homodimeric DNA-Binding and Ligand-Binding Interactions of Human Thyroid Hormone Receptor Justin Taft '13, Andrew Gipson '13, and Patrick Mershon '14
HIV Capsid Protein Kelly Wahl '12 and Kiersten Bell '13


Tyrosine kinase Hck Sarah Cook '11 and Sally Moseley '12
BmrR, A Transcription Activator in Bacillus spp. Emma R. Cummins '13 and Kari N. W. Deininger '13
RNA Polymerase PB1-PB2 subunits from Influenza A Virus Brittany Currey '11 and Lauren Brady '11
The oxidative-stress sensor SoxR bound to DNA Gian Garduque '12 and Jill Pattison '12
Homo sapien Liver X Receptor Beta Kelly Heilman '12 and Crystal Piras '12
Cyclophilin B: A Prolyl Isomerase Shante Jackson '13 and Irene McIntosh '13
E. coli Shiga 2 Toxin Rachel Martin '11 and Daniel Riggins '12
p300/CBP Transcriptional Coactivator David Sowa '12 and Sonam Lhaki '12
Type II Restriction Endonuclease HinP1I Aaron Yeoh '12 and Nathan Huey '13


M. tuberculosis Antigen 85B Kat Meagley '11 and Suzanne Rohrback '11
B. stearothermophilus Adenine DNA Glycosylase Protein MutY Elizabeth Bailey '12 and Jonathan Weil '11 
Fas-FADD Death Domain Complex Jackie Shirreffs '11 and Mac Woods '10 Plasmodium falciparum Histo-Aspartic Protease (HAP) Protein Kerri-Lynn Conrad '11 and Chinagozi Ugwu '10
Sodium-Potassium Pump Monica Kriete '11 and Mary Clare Higgins-Luthman '11


Integration Host Factor
Josh Weber '11 and Phan Truong '11

LAGLIDADG Homing Endonuclease I-CREI
Christian Hinderer '10 and Nora Pencheva '09

Zif268 Zinc Finger Transcription Factor
Robert Carpenter '10 and Emily Nutt '10
Human Tissue Kallikrein 4
Anna Frutiger '09 and Paige Roberts '09
CDK2 in Complex with Synthetic Inhibitors
Jennifer L. Howard '09 and Emily K. Staudenmaier '10
E. coli TolC Multidrug Efflux Pump
Katie Sears '10 and Kristina Buschur '11
HIV-1 Protease and Inhibitor Complex
Kaleb Keyserling '09 and Ken Noguchi '10 
B. subtilis Multidrug Transporter
Jake Calcei '09 and Ben Alexander '09 
Oxytricha nova telomere end-binding protein
Jay Galbraith '09 and Mark Luskus '10


The ?2?2 Antitoxin/Toxin System
Danny Iwamoto '10 and Basil Kahwash '10

p53 Core Domain Bound to DNA
Jane Robertson '08 and Allison Mauk '08
Tetracycline Repressor Complex
Amy Goshe '09 and Sasha Minium '09
Matrix Protein VP40
Sarah Cleeton '09 and Rebecca Cleeton '09
Rho Termination Factor
LaDean Cooley '09 and Piero Sanfilippo '09
Tn5 Transposase
Emma Wampler '09


Human ABAD/HSD10 with Bound Inhibitor, AG10851
Anna Zimmermann '07 and Ann Downer '08
Human BRCT Domain of BRCA1
Brian Steginsky '06 and Alexis Marino '09
Delia Turner '08 and Blaise Milburn '07
Replication Protein A
Amar Desai '08 and Michael Northcutt '08
Plasmodium falciparum Apical Membrane Antigen 1 (AMA1)
Marilyn Haas '08 and Susannah Fulling '08
Human TFIIB in the TFIIB-TBP-TATA-Element Ternary Complex
Josh Cowgill '08, Nick Fanning '08, and Albert Coombs III '07


Pyrococcus furiosus Argonaute
Rebecca Schnitt '05 and Robert Northrup '05
Leptin-E100, the obese protein
Josephine Comas Bardot '08 and Ryan Ruffing '07
Herpes Simplex Thymidine Kinase
Tim O'Neal '07 and Clayton Smith '07
F-93: SSV1 DNA Binding Protein
Emilee Kaser '06 and Liz Narducci '05
Rat Neuronal Nitric Oxide Synthase (nNOS) Reductase Domain
Michael Castle '06 and Adam Sutter '06
Hemagglutinin (HA) - Cell Binding Protein in Avian Influenza
Jack Cerchiara '06 and Brendan Holsberry '07
Diana Spahlinger '07 and Lisa King '07

Jmol-converted tutorials from 1998-2004 Chime Archive

T4 Bacteriophage Cell-Puncturing Device
 Clint Priestley '03 and Matt Schefft '0
Streptococcal Pyrogenic Exotoxin A1
Joel Beckett '08 and Andy Boylan '08
Anthrax Protective Antigen and Lethal Factor
Ansley Scott '02 and Dawn Stancik '02
HIV-1 reverse transcriptase
Oliver Benes '03, 

Rebecca Burke '03, Rebecca Palacios '03
The DNA-Binding Domain of Hin Recombinase Elizabeth E. Millard '98, Aaron Downs '00, and David Marcey
Application loaded.

Archived Chime-based tutorials here.