Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Gene Families01:57

Gene Families

9.2K
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
9.2K
X-ray Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

4.1K
X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
According to Bragg's law, when X-rays strike the sample positioned on a stage, the rays are  scattered by the electron clouds around the sample atoms. The  X-ray diffraction or scattering is caused by constructive interference of the X-ray waves that reflect off the internal...
4.1K
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

44.8K
Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
44.8K
Synthetic Biology02:55

Synthetic Biology

5.0K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
5.0K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Structural insights into θ-type carbonic anhydrases 3 and 4: Tuning the directionality of CO<sub>2</sub> hydration in a diatom.

The FEBS journal·2026
Same author

Crystalline 3D covalent organic frameworks with nbo topology.

Science advances·2026
Same author

Protein Data Bank Japan: A unified portal for integrating structural and chemical data to explore protein-ligand interactions in PDB and PubChem.

Protein science : a publication of the Protein Society·2026
Same author

A planar dimer of bovine ATP synthase.

Cell death and differentiation·2026
Same author

Report of high data rate macromolecular crystallography (HDRMX) meeting, 23 July 2025.

Structural dynamics (Melville, N.Y.)·2026
Same author

Crystal structure determination of an Fe<sup>II</sup> azo aldehyde complex [Fe(C<sub>14</sub>H<sub>11</sub>N<sub>2</sub>O<sub>3</sub>)<sub>2</sub>(H<sub>2</sub>O)<sub>2</sub>] by MicroED.

Acta crystallographica. Section E, Crystallographic communications·2026

Related Experiment Video

Updated: Sep 26, 2025

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

1.6K

PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology.

John D Westbrook1, Jasmine Y Young2, Chenghua Shao2

  • 1Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.

Journal of Molecular Biology
|April 23, 2022
PubMed
Summary

PDBx/mmCIF is the structural biology data standard, enabling FAIR data sharing for 3D macromolecular structures. It supports diverse data types and community-driven development for accelerated scientific discovery.

Keywords:
biological datadata managementdata standardmacromolecular structureprotein data bank (PDB)

More Related Videos

The Automated Crystallography Pipelines at the EMBL HTX Facility in Grenoble
06:50

The Automated Crystallography Pipelines at the EMBL HTX Facility in Grenoble

Published on: June 5, 2021

3.7K
Production, Crystallization, and Structure Determination of the IKK-binding Domain of NEMO
13:02

Production, Crystallization, and Structure Determination of the IKK-binding Domain of NEMO

Published on: December 28, 2019

7.6K

Related Experiment Videos

Last Updated: Sep 26, 2025

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

1.6K
The Automated Crystallography Pipelines at the EMBL HTX Facility in Grenoble
06:50

The Automated Crystallography Pipelines at the EMBL HTX Facility in Grenoble

Published on: June 5, 2021

3.7K
Production, Crystallization, and Structure Determination of the IKK-binding Domain of NEMO
13:02

Production, Crystallization, and Structure Determination of the IKK-binding Domain of NEMO

Published on: December 28, 2019

7.6K

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • PDBx/mmCIF is the established data standard for structural biology, originating from small-molecule crystallography.
  • It is crucial for the deposition, archiving, and dissemination of experimentally determined 3D macromolecular structures by the Worldwide Protein Data Bank (wwPDB).
  • The standard has been extended to accommodate computed models (ModelArchive, AlphaFold), integrative structures (PDB-Dev), and small-angle scattering data (SASBDB).

Purpose of the Study:

  • To describe the architecture, maintenance, governance, and extension processes of the PDBx/mmCIF data standard.
  • To highlight community involvement in the three-decade development of PDBx/mmCIF.
  • To showcase how PDBx/mmCIF facilitates the delivery of Findable, Accessible, Interoperable, and Reusable (FAIR) data.

Main Methods:

  • Description of the PDBx/mmCIF data standard architecture.
  • Overview of tools for maintaining data standard representations.
  • Explanation of governance and extension processes for data content standards.
  • Presentation of community tools and software libraries for data processing and integrity checking.

Main Results:

  • PDBx/mmCIF provides a semantically rich and extensible framework for diverse structural biology data.
  • Community-driven development over three decades has fostered broad adoption and support.
  • The wwPDB utilizes PDBx/mmCIF as the foundation for its FAIR data pipeline, serving millions of users.

Conclusions:

  • PDBx/mmCIF is a vital, evolving data standard essential for modern structural biology.
  • Its comprehensive framework and community support accelerate scientific discovery by enabling robust data sharing.
  • The standard's role in the wwPDB's FAIR data initiatives underscores its importance in the global research community.