8PVB

Structure of GABAAR determined by cryoEM at 100 keV


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit beta-3396Homo sapiensMutation(s): 0 
Gene Names: GABRB3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P28472 (Homo sapiens)
Explore P28472 
Go to UniProtKB:  P28472
PHAROS:  P28472
GTEx:  ENSG00000166206 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28472
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Megabody Mb25B [auth O]522Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC [auth B]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth C]5N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V8D
Query on V8D

Download Ideal Coordinates CCD File 
M [auth A]Etomidate
C14 H16 N2 O2
NPUKDXXFDDZOKR-LLVKDONJSA-N
R16
Query on R16

Download Ideal Coordinates CCD File 
E [auth A]HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
D10
Query on D10

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
HSM
Query on HSM

Download Ideal Coordinates CCD File 
J [auth A]HISTAMINE
C5 H9 N3
NTYJJOPFIAHURM-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTServalcat0.4.27

Structure Validation

View Full Validation Report



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
  • Version 1.2: 2024-01-31
    Changes: Derived calculations, Structure summary