8PVF | pdb_00008pvf

Structure of GAPDH determined by cryoEM at 100 keV


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8PVF

This is version 1.1 of the entry. See complete history

Literature

Structure determination by cryoEM at 100 keV.

McMullan, G.Naydenova, K.Mihaylov, D.Yamashita, K.Peet, M.J.Wilson, H.Dickerson, J.L.Chen, S.Cannone, G.Lee, Y.Hutchings, K.A.Gittins, O.Sobhy, M.A.Wells, T.El-Gomati, M.M.Dalby, J.Meffert, M.Schulze-Briese, C.Henderson, R.Russo, C.J.

(2023) Proc Natl Acad Sci U S A 120: e2312905120-e2312905120

  • DOI: https://doi.org/10.1073/pnas.2312905120
  • Primary Citation Related Structures: 
    8PV9, 8PVA, 8PVB, 8PVC, 8PVD, 8PVE, 8PVF, 8PVG, 8PVH, 8PVI, 8PVJ

  • PubMed Abstract: 

    Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose-built instrument operating at 100 keV-including advances in electron optics, detection, and processing-that makes structure determination fast and simple at a fraction of current costs. The instrument attains its theoretical performance limits, allowing atomic resolution imaging of gold test specimens and biological molecular structure determination in hours. We demonstrate its capabilities by determining the structures of eleven different specimens, ranging in size from 140 kDa to 2 MDa, using a fraction of the data normally required. CryoEM with a microscope designed specifically for high-efficiency, on-the-spot imaging of biological molecules will expand structural biology to a wide range of previously intractable problems.


  • Organizational Affiliation
    • Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 38.72 kDa 
  • Atom Count: 2,535 
  • Modeled Residue Count: 337 
  • Deposited Residue Count: 354 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase354Cryptosporidium parvumMutation(s): 0 
Gene Names: cgd6_37901MB.519CPATCC_002941
EC: 1.2.1.12
UniProt
Find proteins for Q7YYQ9 (Cryptosporidium parvum)
Explore Q7YYQ9 
Go to UniProtKB:  Q7YYQ9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7YYQ9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD



Download:Ideal Coordinates CCD File
B [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTServalcat0.4.27

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC UP 120117
Medical Research Council (MRC, United Kingdom)United KingdomMC U105184322
Wellcome TrustUnited Kingdom220526/B/20/Z
Engineering and Physical Sciences Research CouncilUnited KingdomR122522
Innovate UKUnited Kingdom103806
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/T003677/1

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2023-12-06
    Changes: Database references