What is a Protein? (from PDB-101)
Proteins play countless roles throughout the biological world, from catalyzing chemical reactions to building the structures of all living things. Despite this wide range of functions, all proteins are made out of the same twenty one amino acids, but combined in different ways. The way these twenty amino acids are arranged dictates the folding of the protein into its unique final shape. Since protein function is based on the ability to recognize and bind to specific molecules, having the correct shape is critical for proteins to do their jobs correctly.
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Story by: David S. Goodsell and Maria Voigt
Animation and Editing by: Maria Voigt
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How Enzymes Work (from PDB-101)
Every second inside every living cell, thousands of chemical reactions are taking place. These reactions constitute the essential tasks of life such as metabolism, protein synthesis, cell renewal and growth. Learn how the proteins called enzymes work to maintain the rate of these reactions at a life-sustaining level.
Based on atomic structures from the PDB archive, observe the mechanism of aconitase, an enzyme of the citric acid cycle, to understand how enzymes utilize their amino acid residues to catalyze a reaction.
To learn more about enzymes, explore the educational resources on PDB-101 (
Story by: David S. Goodsell and Maria Voigt
Animation and Video Editing by: Maria Voigt
Narration by: Brian Hudson
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What is a Protein? Learn about the 3D shape and function of macromolecules
A new version of this video is available at
Proteins play countless roles throughout the biological world, from catalyzing chemical reactions to building the structures of all living things.
Despite this wide range of functions all proteins are made out of the same twenty amino acids, but combined in different ways. The way these twenty amino acids are arranged dictates the folding of the protein into its unique final shape. Since protein function is based on the ability to recognize and bind to specific molecules, having the correct shape is critical for proteins to do their jobs correctly.
A PDF flyer accompanies this video at PDB-101 at
Animation by Maria Voigt, narration by Monica Sekharan
Enzymatic reaction (from PDB-101)
In this excerpt from How Enzymes Work, atomic structures from the Protein Data Bank archive are used to show the mechanism of aconitase, an enzyme involved in the breakdown of sugar. It demonstrates how the specific arrangement of amino acids in an enzyme can interact with a small molecule and catalyze a complex chemical reaction. The movie is part of outreach materials on enzyme function and energy metabolism at RCSB PDB-101 (
Watch the entire video at
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You might already know that proteins are a fundamental part of your diet, but they're much more than that.
To learn more about this topic, start your googling with these keywords:
- Amino acids: are organic compounds that contain amino (–NH2) and carboxyl (–COOH) functional groups, along with a side chain specific to each amino acid.
- Proteins: are macromolecules composed of one or more long chains of amino acid residues. Most proteins fold into unique 3D structures. The shape into which a protein naturally folds is known as its native conformation.
- Alpha helix (α-helix): is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues earlier along the protein sequence.
- Beta sheet (β-sheet): is a common motif of the regular protein secondary structure and consists of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet.
- Ribbon diagrams: are 3D schematic representations of protein structure that shows the overall path and organization of the protein backbone in 3D. Ribbon diagrams are generated by interpolating a smooth curve through the polypeptide backbone. α-helices are shown as coiled ribbons or thick tubes, β-strands as arrows, and non-repetitive coils or loops as lines or thin tubes.
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OTHER CREDITS & REFERENCES
Goodsell, David (2006). Visual Methods from Atoms to Cells. Structure 13, Issue 3:347-354. doi:10.1016/j.str.2005.01.012
Protein 3D images created using Mol* ( and structure data from RCSB PDB (
Mol* (D. Sehnal, A.S. Rose, J. Kovca, S.K. Burley, S. Velankar (2018) Mol*: Towards a common library and tools for web molecular graphics MolVA/EuroVis Proceedings. doi:10.2312/molva.20181103)
Villin folding trajectory by Stefan Doerr -
Clathrin Structure (PDB ID: 3IYV)
Fotin, A., et al (2004). Molecular model for a complete clathrin lattice from electron cryomicroscopy. Nature 432: 573-579. doi:10.1038/nature03079
Immunoglobulin Structure (PDB IDs: 1IGT & 1IGY)
Harris, L.J., et al (1998). Crystallographic structure of an intact IgG1 monoclonal antibody. J Mol Biol 275: 861-872. doi:10.1006/jmbi.1997.1508
ATP Synthase Structure (PDB IDs: 5ARE, 5ARI & 5FIL)
Zhou, A., et al (2015). Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM. ELife, 4. doi:10.7554/eLife.10180
RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) -
Photosystem II (PDB ID: 5XNL)
Su, X., et al (2017). Structure and assembly mechanism of plant C2S2M2-type PSII-LHCII supercomplex. Science 357: 815-820. doi:10.1126/science.aan0327
Ribonuclease (PDB ID: 2AAS)
Santoro, J., et al (1993). High-resolution three-dimensional structure of ribonuclease A in solution by nuclear magnetic resonance spectroscopy. J Mol Biol 229: 722-734. doi:10.1006/jmbi.1993.1075
Myosin (PDB ID: 1B7T)
Houdusse, A., et al (1999). Atomic structure of scallop myosin subfragment S1 complexed with MgADP: a novel conformation of the myosin head. Cell 97: 459-470. doi:10.1016/s0092-8674(00)80756-4
Neuronal Signaling and Sodium-Potassium Pump (from PDB-101)
Our neurons use electrical impulses and complex molecular machinery to communicate information throughout our bodies. In order to be ready to transfer the signal when it arrives, the neurons need to maintain high concentrations of sodium on the outside of the membrane and potassium ions on the inside. With each signal transmission, sodium enters the neuron followed by potassium exiting the cell.
The sodium potassium pump is a transport protein that regulates and restores the gradients of sodium and potassium ions across the membrane. With each pumping cycle, it transports 2 potassium ions back into the cell, and 3 sodium ions out of the cell.
Using structures from the Protein Data Bank, this animation shows how the essential proteins work together to prepare for and conduct the neuronal signal. The video zooms in on the mechanism sodium-potassium pump to explore the concept of the active membrane transport.
To learn more about the proteins shown in this video, visit PDB-101 ( and read the Molecule of the Month articles on Voltage-gated Sodium Channel ( Potassium Channels ( and Sodium-Potassium Pump (
How to fold PDB-101's DNA paper model
RCSB PDB's intern Nicole Brennan demonstrates her origami skills to build a 3D paper model of DNA.
Download the PDF model from along with the Molecule of the Month's DNA article.
The paper model and article are also available in Spanish.
PDB-101 packages together resources that promote exploration in the world of proteins and nucleic acids for teachers, students, and the general public.
Tour of the resources at PDB-101
Learn about the different resources available at PDB-101, the educational view of the RCSB PDB website. PDB-101 and the RCSB PDB are tools for understanding biomacromolecules and biology at the structural level.
Ebola Virus Proteins (from PDB-101)
Tour the molecular anatomy of the Ebola virus with the RCSB PDB. Understanding of the shape and structure of the proteins that make up Ebola is a key component in the fight against the virus. Learn more at Molecule of the Month:
Penicillin and Antibiotic Resistance (from PDB-101)
Since its discovery in 1928, penicillin and penicillin-related antibiotics helped save countless lives from bacterial infections. However, in the face of overuse and misuse of antibiotics, bacteria evolved resistance mechanisms that allow them to proliferate even in the presence of the newest antibiotics. Watch this video to learn how penicillin and penicillin-related antibiotics disrupt the bacterial life cycle, and what molecular mechanisms bacteria employ to evade the action of these drugs.
Learn more about antibiotic resistance from PDB-101
Story by: Stephen K. Burley, David S. Goodsell, Maria Voigt
Animation and Video Editing: Maria Voigt
Narration: Brian Hudson
How to get a protein PDB file from protein data bank?
as a part of VMD tutorial series , in this video we learn how to download pdb file from protein data bank.
What are proteins? Proteins are an essential part of the human diet. They are found in a variety of foods like eggs, dairy, seafood, legumes, meats, nuts, and seeds. Regardless of the source, the protein that we eat gets broken down and reformed into new proteins in our bodies.
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Fighting Coronavirus with Soap (from PDB-101)
Always use soap when you wash your hands! Soap molecules break up the outer layer of enveloped viruses, stopping infection. Watch at the molecular level how soap breaks up coronavirus by using series of hydrophilic and hydrophobic interactions.
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We produced the video in record time and that's when mistakes happen. If you are wondering about the blurs popping up here and there, here is the explanation:
0:34 The word 'micelle' was misspelled. We don't want to reinforce the learning of the bad spelling of this word.
0:49 The depiction is of the M (membrane) protein, which is involved in capturing and organizing the genomic RNA during budding. The PDB entry 1zva is was used to model the M protein.
We apologize for the mistakes.
Protein Structure and Folding
After a polypeptide is produced in protein synthesis, it's not necessarily a functional protein yet! Explore protein folding that occurs within levels of protein structure with the Amoeba Sisters! Primary, secondary, tertiary, and quaternary protein structure levels are briefly discussed. Video also mentions chaperonins (chaperone proteins) and how proteins can be denatured.
Table of Contents:
0:41 Reminder of Protein Roles
1:06 Modifications of Proteins
1:25 Importance of Shape for Proteins
1:56 Levels of Protein Structure
2:06 Primary Structure
3:10 Secondary Structure
3:45 Tertiary Structure
4:58 Quaternary Structure [not in all proteins]
6:01 Proteins often have help in folding [introduces chaperonins]
6:40 Denaturing Proteins
*Further Reading Suggestions*
Related to Protein Misfoldings:
Learn About The Protein Folding Problem:
OpenStax, Biology. OpenStax CNX. Jun 1, 2018
Reece, J. B., & Campbell, N. A. (2011). Campbell biology. Boston: Benjamin Cummings / Pearson.
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Calcium Pump (from PDB-101)
This animation is an excerpt from the What is a Protein? video available here:
Animation by Maria Voigt
Nutrition 101 Series – What is Protein?
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Protein is one of the most important, if not the most important nutrient in your healthy eating plan.
I will show you in our short guide, what Protein is and how it can help you in whatever main health & fitness goal you have.
So let's dive in and see why Protein is so important.
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Basic Guide to Protein Data Bank and PDB files
This video includes a basic guide to Protein Data Bank and PDB data: asymmetric unit, biological assembly, chains, molecules, resolution, organism, method, header record, coordinate records and so on.
Readers! Do You Read by Chris Zabriskie is licensed under a Creative Commons Attribution licence (
PDB-101 Video challenge 2017
Treatments of type 2 diabetes
How to Use Protein Data Bank | What is PDB | PyMol Series | Part-1 | Basic Science Series
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organizations.
The PDB is key in areas of structural biologies, such as structural genomics. Most major scientific journals, and some funding agencies, now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB. For example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology.
PyMOL is an open-source molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. According to the original author, by 2009, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL
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Protein Data Bank (PDB): Tutorial - Parte 1
Nesse vídeo, faremos um tour virtual no site do PDB, onde serão apresentadas as principais funcionalidades relacionadas a busca por complexos e pelas informações que podem ser adquiridas nesse banco de dados.
No próximo vídeo dessa série, serão abordados o modo de visualização e também o site do PDBSum.