8PVB | pdb_00008pvb

Structure of GABAAR determined by cryoEM at 100 keV

PDB DOI: https://doi.org/10.2210/pdb8PVB/pdb
EM Map EMD-17960: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Lama glama
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2023-07-17 Released: 2023-11-29
Deposition Author(s): McMullan, G., Naydenova, K., Mihaylov, D., Peet, M.J., Wilson, H., Yamashita, K., Dickerson, J.L., Chen, S., Cannone, G., Lee, Y., Hutchings, K.A., Gittins, O., Sobhy, M., Wells, T., El-Gomati, M.M., Dalby, J., Meffert, M., Schulze-Briese, C., Henderson, R., Russo, C.J.
Funding Organization(s): Medical Research Council (MRC, United Kingdom), Wellcome Trust, Engineering and Physical Sciences Research Council, Innovate UK, Biotechnology and Biological Sciences Research Council (BBSRC)

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 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

PubMed: 38011573 Search on PubMed Search on PubMed Central
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: 104.6 kDa
Atom Count: 3,845
Modeled Residue Count: 455
Deposited Residue Count: 918
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid receptor subunit beta-3	A	396	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28472
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A	Go to GlyGen: P28472-1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Megabody Mb25	B [auth O]	522	Lama glama	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B]	2		N-Glycosylation	Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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-glucopyranose	D [auth C]	5		N-Glycosylation	Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
V8D Query on V8D Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	Etomidate C₁₄ H₁₆ N₂ O₂ NPUKDXXFDDZOKR-LLVKDONJSA-N		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
R16 Query on R16 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
D10 Query on D10 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
HSM Query on HSM Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	HISTAMINE C₅ H₉ N₃ NTYJJOPFIAHURM-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	K [auth A], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain K [auth A] Focus chain L [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
V8D	BindingDB: 8PVB	IC50: 5.77e+5 (nM) from 1 assay(s)
V8D	BindingDB: 8PVB	EC50: min: 1200, max: 6.40e+4 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Servalcat	0.4.27

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-11-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC UP 120117
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC U105184322
Wellcome Trust	United Kingdom	220526/B/20/Z
Engineering and Physical Sciences Research Council	United Kingdom	R122522
Innovate UK	United Kingdom	103806
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/T003677/1