4TNV

C. elegans glutamate-gated chloride channel (GluCl) in complex with Fab in a non-conducting conformation

PDB DOI: https://doi.org/10.2210/pdb4TNV/pdb

Classification: Transport Protein/immune System
Organism(s): Caenorhabditis elegans, Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2014-06-05 Released: 2014-08-13
Deposition Author(s): Althoff, T., Hibbs, R.E., Banerjee, S., Gouaux, E.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), German Research Foundation (DFG), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free: 0.283
R-Value Work: 0.261
R-Value Observed: 0.262

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 878.62 kDa
Atom Count: 60,408
Modelled Residue Count: 7,719
Deposited Residue Count: 7,860
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Avermectin-sensitive glutamate-gated chloride channel GluCl alpha	A B C D E A, B, C, D, E, M [auth P], N [auth Q], O [auth R], P [auth S], Q [auth T]	347	Caenorhabditis elegans	Mutation(s): 0 Gene Names: glc-1, CELE_F11A5.10, F11A5.10 Membrane Entity: Yes
UniProt
Find proteins for G5EBR3 (Caenorhabditis elegans) Explore G5EBR3 Go to UniProtKB: G5EBR3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G5EBR3
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mouse monoclonal Fab fragment, heavy chain	BA [auth J] CA [auth I] F G H BA [auth J], CA [auth I], F, G, H, R [auth U], S [auth V], T [auth W], U [auth X], V [auth Y]	224	Mus musculus	Mutation(s): 0
Entity Groups
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mouse monoclonal Fab fragment, light chain	AA [auth i] DA [auth M] I [auth K] J [auth L] K [auth N] AA [auth i], DA [auth M], I [auth K], J [auth L], K [auth N], L [auth O], W [auth Z], X [auth f], Y [auth g], Z [auth h]	215	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain FA [auth A] SDF format, chain QA [auth P] SDF format, chain AB [auth T] SDF format, chain IA [auth B] SDF format, chain KA [auth C] SDF format, chain MA [auth D] SDF format, chain OA [auth E] SDF format, chain UA [auth Q] SDF format, chain WA [auth R] SDF format, chain YA [auth S] MOL2 format, chain FA [auth A] MOL2 format, chain QA [auth P] MOL2 format, chain AB [auth T] MOL2 format, chain IA [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain OA [auth E] MOL2 format, chain UA [auth Q] MOL2 format, chain WA [auth R] MOL2 format, chain YA [auth S]	AB [auth T] FA [auth A] IA [auth B] KA [auth C] MA [auth D] AB [auth T], FA [auth A], IA [auth B], KA [auth C], MA [auth D], OA [auth E], QA [auth P], UA [auth Q], WA [auth R], YA [auth S]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain AB [auth T] Focus chain FA [auth A] Focus chain IA [auth B] Focus chain KA [auth C] Focus chain MA [auth D] Focus chain OA [auth E] Focus chain QA [auth P] Focus chain UA [auth Q] Focus chain WA [auth R] Focus chain YA [auth S] Interactions & Density Focus chain AB [auth T] Focus chain FA [auth A] Focus chain IA [auth B] Focus chain KA [auth C] Focus chain MA [auth D] Focus chain OA [auth E] Focus chain QA [auth P] Focus chain UA [auth Q] Focus chain WA [auth R] Focus chain YA [auth S]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain VA [auth R] SDF format, chain EA [auth A] SDF format, chain HA [auth B] SDF format, chain JA [auth C] SDF format, chain LA [auth D] SDF format, chain NA [auth E] SDF format, chain PA [auth P] SDF format, chain TA [auth Q] SDF format, chain XA [auth S] SDF format, chain ZA [auth T] MOL2 format, chain VA [auth R] MOL2 format, chain EA [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain JA [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain NA [auth E] MOL2 format, chain PA [auth P] MOL2 format, chain TA [auth Q] MOL2 format, chain XA [auth S] MOL2 format, chain ZA [auth T]	EA [auth A] HA [auth B] JA [auth C] LA [auth D] NA [auth E] EA [auth A], HA [auth B], JA [auth C], LA [auth D], NA [auth E], PA [auth P], TA [auth Q], VA [auth R], XA [auth S], ZA [auth T]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain EA [auth A] Focus chain HA [auth B] Focus chain JA [auth C] Focus chain LA [auth D] Focus chain NA [auth E] Focus chain PA [auth P] Focus chain TA [auth Q] Focus chain VA [auth R] Focus chain XA [auth S] Focus chain ZA [auth T] Interactions & Density Focus chain EA [auth A] Focus chain HA [auth B] Focus chain JA [auth C] Focus chain LA [auth D] Focus chain NA [auth E] Focus chain PA [auth P] Focus chain TA [auth Q] Focus chain VA [auth R] Focus chain XA [auth S] Focus chain ZA [auth T]
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain BB [auth T] SDF format, chain GA [auth A] MOL2 format, chain BB [auth T] MOL2 format, chain GA [auth A]	BB [auth T], GA [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain BB [auth T] Focus chain GA [auth A] Interactions & Density Focus chain BB [auth T] Focus chain GA [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain RA [auth P] SDF format, chain SA [auth P] MOL2 format, chain RA [auth P] MOL2 format, chain SA [auth P]	RA [auth P], SA [auth P]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain RA [auth P] Focus chain SA [auth P] Interactions & Density Focus chain RA [auth P] Focus chain SA [auth P]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.60 Å
R-Value Free: 0.283
R-Value Work: 0.261
R-Value Observed: 0.262
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 455.81	α = 90
b = 195.68	β = 93.15
c = 196.18	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2014-08-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5 R01 GM100400
German Research Foundation (DFG)	Germany	AL 1725-1/1
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	F32NS061404

Revision History (Full details and data files)

Version 1.0: 2014-08-13
Type: Initial release
Version 1.1: 2014-09-03
Changes: Database references
Version 1.2: 2017-09-27
Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
Version 1.3: 2019-12-18
Changes: Author supporting evidence
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Refinement description, Structure summary
Version 1.5: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary

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4TNV

C. elegans glutamate-gated chloride channel (GluCl) in complex with Fab in a non-conducting conformation

Entity ID: 1

UniProt

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Sequence Annotations

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Entity ID: 2

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Entity ID: 3

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

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