[English] 日本語
Yorodumi
- PDB-4tnv: C. elegans glutamate-gated chloride channel (GluCl) in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tnv
TitleC. elegans glutamate-gated chloride channel (GluCl) in complex with Fab in a non-conducting conformation
Components
  • (Mouse monoclonal Fab fragment, ...) x 2
  • Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
KeywordsTransport Protein/immune System / membrane protein / ligand-gated ion channel / neurotransmitter receptor / Cys-loop receptor / Transport Protein-immune System complex
Function / homology
Function and homology information


extracellularly glutamate-gated chloride channel activity / Neurotransmitter receptors and postsynaptic signal transmission / locomotion involved in locomotory behavior / glutamate binding / neurotransmitter receptor activity / protein complex oligomerization / transmembrane transporter complex / chloride transmembrane transport / transmembrane signaling receptor activity / postsynaptic membrane ...extracellularly glutamate-gated chloride channel activity / Neurotransmitter receptors and postsynaptic signal transmission / locomotion involved in locomotory behavior / glutamate binding / neurotransmitter receptor activity / protein complex oligomerization / transmembrane transporter complex / chloride transmembrane transport / transmembrane signaling receptor activity / postsynaptic membrane / neuron projection / synapse / identical protein binding / plasma membrane
Similarity search - Function
Glutamate gated chloride channel, transmembrane domain / Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily ...Glutamate gated chloride channel, transmembrane domain / Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Distorted Sandwich / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CITRATE ANION / Glutamate-gated chloride channel alpha
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsAlthoff, T. / Hibbs, R.E. / Banerjee, S. / Gouaux, E.
Funding support United States, Germany, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 R01 GM100400 United States
German Research Foundation (DFG)AL 1725-1/1 Germany
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F32NS061404 United States
Citation
Journal: Nature / Year: 2014
Title: X-ray structures of GluCl in apo states reveal a gating mechanism of Cys-loop receptors.
Authors: Althoff, T. / Hibbs, R.E. / Banerjee, S. / Gouaux, E.
#1: Journal: Nature / Year: 2011
Title: Principles of activation and permeation in an anion-selective Cys-loop receptor.
Authors: Hibbs, R.E. / Gouaux, E.
History
DepositionJun 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / entity_src_nat / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity.pdbx_description ..._citation.journal_id_CSD / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
B: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
C: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
D: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
E: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
F: Mouse monoclonal Fab fragment, heavy chain
G: Mouse monoclonal Fab fragment, heavy chain
H: Mouse monoclonal Fab fragment, heavy chain
K: Mouse monoclonal Fab fragment, light chain
L: Mouse monoclonal Fab fragment, light chain
N: Mouse monoclonal Fab fragment, light chain
O: Mouse monoclonal Fab fragment, light chain
P: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
Q: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
R: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
S: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
T: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
U: Mouse monoclonal Fab fragment, heavy chain
V: Mouse monoclonal Fab fragment, heavy chain
W: Mouse monoclonal Fab fragment, heavy chain
X: Mouse monoclonal Fab fragment, heavy chain
Y: Mouse monoclonal Fab fragment, heavy chain
Z: Mouse monoclonal Fab fragment, light chain
f: Mouse monoclonal Fab fragment, light chain
g: Mouse monoclonal Fab fragment, light chain
h: Mouse monoclonal Fab fragment, light chain
i: Mouse monoclonal Fab fragment, light chain
J: Mouse monoclonal Fab fragment, heavy chain
I: Mouse monoclonal Fab fragment, heavy chain
M: Mouse monoclonal Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)878,62354
Polymers870,85530
Non-polymers7,76724
Water00
1
A: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
B: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
C: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
D: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
E: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
F: Mouse monoclonal Fab fragment, heavy chain
G: Mouse monoclonal Fab fragment, heavy chain
H: Mouse monoclonal Fab fragment, heavy chain
K: Mouse monoclonal Fab fragment, light chain
L: Mouse monoclonal Fab fragment, light chain
N: Mouse monoclonal Fab fragment, light chain
O: Mouse monoclonal Fab fragment, light chain
J: Mouse monoclonal Fab fragment, heavy chain
I: Mouse monoclonal Fab fragment, heavy chain
M: Mouse monoclonal Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,27626
Polymers435,42815
Non-polymers3,84811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
P: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
Q: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
R: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
S: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
T: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
U: Mouse monoclonal Fab fragment, heavy chain
V: Mouse monoclonal Fab fragment, heavy chain
W: Mouse monoclonal Fab fragment, heavy chain
X: Mouse monoclonal Fab fragment, heavy chain
Y: Mouse monoclonal Fab fragment, heavy chain
Z: Mouse monoclonal Fab fragment, light chain
f: Mouse monoclonal Fab fragment, light chain
g: Mouse monoclonal Fab fragment, light chain
h: Mouse monoclonal Fab fragment, light chain
i: Mouse monoclonal Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)439,34728
Polymers435,42815
Non-polymers3,91913
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)455.810, 195.680, 196.180
Angle α, β, γ (deg.)90.00, 93.15, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 1:300 )
21chain B and (resseq 1:300 )
31chain C and (resseq 1:300 )
41chain D and (resseq 1:300 )
51chain E and (resseq 1:300 )
61chain P and (resseq 1:300 )
71chain Q and (resseq 1:300 )
81chain R and (resseq 1:300 )
91chain S and (resseq 1:300 )
101chain T and (resseq 1:300 )
12chain A and (resseq 314:340 )
22chain B and (resseq 314:340 )
32chain C and (resseq 314:340 )
42chain D and (resseq 314:340 )
52chain E and (resseq 314:340 )
62chain P and (resseq 314:340 )
72chain Q and (resseq 314:340 )
82chain R and (resseq 314:340 )
92chain S and (resseq 314:340 )
102chain T and (resseq 314:340 )
13chain F and (resseq 1:120 )
23chain G and (resseq 1:120 )
33chain H and (resseq 1:120 )
43chain I and (resseq 1:120 )
53chain J and (resseq 1:120 )
63chain U and (resseq 1:120 )
73chain V and (resseq 1:120 )
83chain W and (resseq 1:120 )
93chain X and (resseq 1:120 )
103chain Y and (resseq 1:120 )
14chain K and (resseq 1:108 )
24chain L and (resseq 1:108 )
34chain M and (resseq 1:108 )
44chain N and (resseq 1:108 )
54chain O and (resseq 1:108 )
64chain Z and (resseq 1:108 )
74chain f and (resseq 1:108 )
84chain g and (resseq 1:108 )
94chain h and (resseq 1:108 )
104chain i and (resseq 1:108 )

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERILEILEchain A and (resseq 1:300 )AA1 - 3001 - 300
21SERSERILEILEchain B and (resseq 1:300 )BB1 - 3001 - 300
31SERSERILEILEchain C and (resseq 1:300 )CC1 - 3001 - 300
41SERSERILEILEchain D and (resseq 1:300 )DD1 - 3001 - 300
51SERSERILEILEchain E and (resseq 1:300 )EE1 - 3001 - 300
61SERSERILEILEchain P and (resseq 1:300 )PM1 - 3001 - 300
71SERSERILEILEchain Q and (resseq 1:300 )QN1 - 3001 - 300
81SERSERILEILEchain R and (resseq 1:300 )RO1 - 3001 - 300
91SERSERILEILEchain S and (resseq 1:300 )SP1 - 3001 - 300
101SERSERILEILEchain T and (resseq 1:300 )TQ1 - 3001 - 300
12ARGARGHISHISchain A and (resseq 314:340 )AA314 - 340314 - 340
22ARGARGHISHISchain B and (resseq 314:340 )BB314 - 340314 - 340
32ARGARGHISHISchain C and (resseq 314:340 )CC314 - 340314 - 340
42ARGARGHISHISchain D and (resseq 314:340 )DD314 - 340314 - 340
52ARGARGHISHISchain E and (resseq 314:340 )EE314 - 340314 - 340
62ARGARGHISHISchain P and (resseq 314:340 )PM314 - 340314 - 340
72ARGARGHISHISchain Q and (resseq 314:340 )QN314 - 340314 - 340
82ARGARGHISHISchain R and (resseq 314:340 )RO314 - 340314 - 340
92ARGARGHISHISchain S and (resseq 314:340 )SP314 - 340314 - 340
102ARGARGHISHISchain T and (resseq 314:340 )TQ314 - 340314 - 340
13GLUGLUVALVALchain F and (resseq 1:120 )FF1 - 1201 - 120
23GLUGLUVALVALchain G and (resseq 1:120 )GG1 - 1201 - 120
33GLUGLUVALVALchain H and (resseq 1:120 )HH1 - 1201 - 120
43GLUGLUVALVALchain I and (resseq 1:120 )ICA1 - 1201 - 120
53GLUGLUVALVALchain J and (resseq 1:120 )JBA1 - 1201 - 120
63GLUGLUVALVALchain U and (resseq 1:120 )UR1 - 1201 - 120
73GLUGLUVALVALchain V and (resseq 1:120 )VS1 - 1201 - 120
83GLUGLUVALVALchain W and (resseq 1:120 )WT1 - 1201 - 120
93GLUGLUVALVALchain X and (resseq 1:120 )XU1 - 1201 - 120
103GLUGLUVALVALchain Y and (resseq 1:120 )YV1 - 1201 - 120
14GLNGLNVALVALchain K and (resseq 1:108 )KI1 - 1081 - 108
24GLNGLNVALVALchain L and (resseq 1:108 )LJ1 - 1081 - 108
34GLNGLNVALVALchain M and (resseq 1:108 )MDA1 - 1081 - 108
44GLNGLNVALVALchain N and (resseq 1:108 )NK1 - 1081 - 108
54GLNGLNVALVALchain O and (resseq 1:108 )OL1 - 1081 - 108
64GLNGLNVALVALchain Z and (resseq 1:108 )ZW1 - 1081 - 108
74GLNGLNVALVALchain f and (resseq 1:108 )fX1 - 1081 - 108
84GLNGLNVALVALchain g and (resseq 1:108 )gY1 - 1081 - 108
94GLNGLNVALVALchain h and (resseq 1:108 )hZ1 - 1081 - 108
104GLNGLNVALVALchain i and (resseq 1:108 )iAA1 - 1081 - 108

NCS ensembles :
ID
1
2
3
4

-
Components

-
Protein , 1 types, 10 molecules ABCDEPQRST

#1: Protein
Avermectin-sensitive glutamate-gated chloride channel GluCl alpha / Protein GLC-1


Mass: 39636.629 Da / Num. of mol.: 10 / Fragment: UNP residues 62-363,UNP residues 422-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: glc-1, CELE_F11A5.10, F11A5.10 / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Organ (production host): Ovary / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): Ovary / References: UniProt: G5EBR3

-
Antibody , 2 types, 20 molecules FGHUVWXYJIKLNOZfghiM

#2: Antibody
Mouse monoclonal Fab fragment, heavy chain


Mass: 24297.170 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma
#3: Antibody
Mouse monoclonal Fab fragment, light chain


Mass: 23151.738 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma

-
Sugars , 2 types, 20 molecules

#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 2 types, 4 molecules

#6: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

-
Details

Has protein modificationY
Sequence detailsUNP G5EBR3 residues 364-421 are replaced with residues AGT

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 5.02 Å3/Da / Density % sol: 75.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 35-36% pentaerythritol propoxylate (5/4 PO/OH), 50 mM sodium citrate pH 5.5, 100 mM potassium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2011
Details: Mirrors: bent cylinders, stripes of Pt, Rh and clear
RadiationMonochromator: Cryo-cooled double Si(111) crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.6→58.44 Å / Num. obs: 175651 / % possible obs: 88.4 % / Redundancy: 1.85 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 5.82
Reflection shellResolution: 3.6→3.64 Å / Redundancy: 1.54 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 1.37 / % possible all: 78.9

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RHW

3rhw


Resolution: 3.6→58.438 Å / SU ML: 0.75 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 33.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2829 8778 5 %random
Rwork0.2611 ---
obs0.2622 175580 88.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→58.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms60008 0 400 0 60408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00462049
X-RAY DIFFRACTIONf_angle_d0.78384673
X-RAY DIFFRACTIONf_dihedral_angle_d11.15521778
X-RAY DIFFRACTIONf_chiral_restr0.0319851
X-RAY DIFFRACTIONf_plane_restr0.00510524
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2360X-RAY DIFFRACTIONPOSITIONAL0.013
12B2360X-RAY DIFFRACTIONPOSITIONAL0.013
13C2360X-RAY DIFFRACTIONPOSITIONAL0.012
14D2360X-RAY DIFFRACTIONPOSITIONAL0.012
15E2360X-RAY DIFFRACTIONPOSITIONAL0.012
16P2360X-RAY DIFFRACTIONPOSITIONAL0.014
17Q2360X-RAY DIFFRACTIONPOSITIONAL0.013
18R2360X-RAY DIFFRACTIONPOSITIONAL0.013
19S2360X-RAY DIFFRACTIONPOSITIONAL0.017
110T2360X-RAY DIFFRACTIONPOSITIONAL0.013
21A237X-RAY DIFFRACTIONPOSITIONAL0.011
22B237X-RAY DIFFRACTIONPOSITIONAL0.011
23C237X-RAY DIFFRACTIONPOSITIONAL0.01
24D237X-RAY DIFFRACTIONPOSITIONAL0.01
25E237X-RAY DIFFRACTIONPOSITIONAL0.012
26P237X-RAY DIFFRACTIONPOSITIONAL0.013
27Q237X-RAY DIFFRACTIONPOSITIONAL0.013
28R237X-RAY DIFFRACTIONPOSITIONAL0.013
29S237X-RAY DIFFRACTIONPOSITIONAL0.014
210T237X-RAY DIFFRACTIONPOSITIONAL0.012
31F949X-RAY DIFFRACTIONPOSITIONAL0.104
32G949X-RAY DIFFRACTIONPOSITIONAL0.104
33H949X-RAY DIFFRACTIONPOSITIONAL0.148
34I949X-RAY DIFFRACTIONPOSITIONAL0.104
35J949X-RAY DIFFRACTIONPOSITIONAL0.237
36U949X-RAY DIFFRACTIONPOSITIONAL0.104
37V949X-RAY DIFFRACTIONPOSITIONAL0.104
38W949X-RAY DIFFRACTIONPOSITIONAL0.104
39X949X-RAY DIFFRACTIONPOSITIONAL0.104
310Y949X-RAY DIFFRACTIONPOSITIONAL0.012
41K804X-RAY DIFFRACTIONPOSITIONAL0.439
42L804X-RAY DIFFRACTIONPOSITIONAL0.439
43M804X-RAY DIFFRACTIONPOSITIONAL0.165
44N804X-RAY DIFFRACTIONPOSITIONAL0.192
45O804X-RAY DIFFRACTIONPOSITIONAL0.236
46Z804X-RAY DIFFRACTIONPOSITIONAL0.235
47f804X-RAY DIFFRACTIONPOSITIONAL0.167
48g804X-RAY DIFFRACTIONPOSITIONAL0.237
49h804X-RAY DIFFRACTIONPOSITIONAL0.169
410i804X-RAY DIFFRACTIONPOSITIONAL0.242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.64090.40092590.40874929X-RAY DIFFRACTION78
3.6409-3.68370.41412620.41184960X-RAY DIFFRACTION79
3.6837-3.72860.40452610.40014976X-RAY DIFFRACTION80
3.7286-3.77580.41682690.39635100X-RAY DIFFRACTION81
3.7758-3.82550.39342660.39035048X-RAY DIFFRACTION81
3.8255-3.87790.39162670.38515088X-RAY DIFFRACTION81
3.8779-3.93330.40852710.38375152X-RAY DIFFRACTION83
3.9333-3.9920.39292760.37385234X-RAY DIFFRACTION83
3.992-4.05430.37192810.36585336X-RAY DIFFRACTION85
4.0543-4.12080.33462840.33565403X-RAY DIFFRACTION86
4.1208-4.19180.32372930.32445561X-RAY DIFFRACTION88
4.1918-4.2680.33372940.32255594X-RAY DIFFRACTION89
4.268-4.35010.34852940.31565588X-RAY DIFFRACTION89
4.3501-4.43890.31352980.29425652X-RAY DIFFRACTION90
4.4389-4.53540.26143020.28375739X-RAY DIFFRACTION92
4.5354-4.64080.293010.2675719X-RAY DIFFRACTION91
4.6408-4.75680.2553050.25665806X-RAY DIFFRACTION92
4.7568-4.88540.2633070.24595818X-RAY DIFFRACTION92
4.8854-5.02910.25343060.23675821X-RAY DIFFRACTION93
5.0291-5.19130.25513080.23815861X-RAY DIFFRACTION93
5.1913-5.37670.26733090.24915861X-RAY DIFFRACTION93
5.3767-5.59180.27493100.24695889X-RAY DIFFRACTION93
5.5918-5.84610.26663070.24295834X-RAY DIFFRACTION93
5.8461-6.1540.26463090.25175865X-RAY DIFFRACTION93
6.154-6.53910.27593070.24135840X-RAY DIFFRACTION92
6.5391-7.04320.25863090.24465867X-RAY DIFFRACTION93
7.0432-7.75050.27413110.21635913X-RAY DIFFRACTION93
7.7505-8.86870.22613090.1915872X-RAY DIFFRACTION93
8.8687-11.16090.1693100.15335881X-RAY DIFFRACTION93
11.1609-58.44590.2852930.24025595X-RAY DIFFRACTION86
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.02920.62891.48862.37541.07983.3227-0.05-0.36270.15150.2841-0.269-0.1372-0.5361-0.00680.33120.681-0.03980.01370.78360.23721.0702-65.3085-31.505614.0097
22.8517-0.61020.25521.2782-0.90762.9897-0.2130.06510.28550.1705-0.3051-0.3294-0.12720.81430.5020.74910.0116-0.00310.80780.17250.9016-84.9197-31.283830.5929
32.1264-0.33641.24731.93110.19753.6920.26860.08080.0030.4527-0.0358-0.42330.08770.6616-0.1421.075-0.15450.07330.8788-0.10670.7483-91.0812-6.911534.773
41.4322-0.12720.91921.3495-0.45423.83750.3881-0.2658-0.5430.4305-0.1677-0.16180.28950.0051-0.1871.0895-0.3723-0.10620.9086-0.1391.1894-75.30537.915721.1687
51.84740.2550.211.54060.33592.869-0.1482-0.67140.07780.1014-0.1775-0.048-0.1380.0150.38730.6999-0.1582-0.07660.95980.06531.1881-59.3285-7.53978.4657
61.7572-0.009-0.27540.97830.92312.07320.5116-0.8362-0.27220.5848-0.5190.22120.0692-0.06990.03761.3871-0.29610.08511.52120.0921.1955-133.7583-40.144947.0154
70.8673-0.52340.03221.31070.35831.09860.4299-0.13290.9192-0.69070.1064-0.683-1.0574-0.2918-0.23642.0441-0.02850.45041.10230.07521.3555-124.105433.979435.6571
81.43830.3740.51194.0077-0.58051.71820.5173-0.0587-0.2026-0.1512-0.26820.66940.334-0.2812-0.22510.70220.018-0.00930.84470.11281.1299-80.5595-80.57121.8069
92.53740.1265-1.30141.9437-1.23242.23580.3241-0.0880.26060.3689-0.6213-0.6414-0.55620.43430.32591.2191-0.1809-0.13090.99560.0111.331-61.987842.4088-15.7129
102.6887-1.1448-1.18961.33611.65882.2144-0.2053-0.181-0.2059-0.3188-0.15570.3973-0.6752-0.34850.01481.58980.08370.20291.0245-0.02521.0994-136.651622.691739.2391
110.1687-0.5502-0.10594.55190.12371.72350.31980.2074-0.2795-1.06810.090.33910.37680.0487-0.36840.95210.2227-0.1650.85850.14151.0681-71.8626-78.7659-13.3333
121.08551.196-0.29681.30550.18541.16290.0724-0.5141-0.70430.6397-0.4634-0.16390.4044-0.02760.2091.4923-0.08690.07741.12630.21111.5258-133.0558-55.488639.0465
130.9352-0.2427-0.51822.3499-1.04210.65380.1980.10210.37540.51570.0083-0.5178-0.6798-0.0632-0.0661.0822-0.225-0.06940.9564-0.1751.082-76.569851.4825-11.8144
140.6663-0.32670.38721.67790.53583.71260.0175-0.0622-0.01360.18720.05930.0267-0.04330.2721-0.1270.68260.12160.07981.00650.00460.7246-50.431996.970468.6049
152.4470.02831.29171.5326-0.37473.0888-0.1251-0.47730.07660.02990.1110.1899-0.08010.02650.01060.6236-0.01140.05930.90030.05690.8582-52.309971.519469.9861
162.8953-0.56522.16142.0908-1.11542.9039-0.169-0.0498-0.18760.20210.1025-0.1004-0.17730.0050.02130.6915-0.01840.05890.7801-0.11680.7907-33.971861.365855.3967
173.3750.17251.8260.83670.32172.01180.147-0.7318-0.05050.0144-0.0131-0.06880.1755-0.2785-0.15280.6946-0.04830.05190.902-0.070.5625-20.734680.67444.7273
181.94480.62011.18071.69530.3223.29650.1235-0.38350.05430.1923-0.161-0.1678-0.30710.17270.02020.81780.0388-0.05530.6503-0.04380.5855-30.7931102.514252.9955
190.1798-0.35430.09541.45930.43090.10820.2471-0.3466-0.471-0.29220.05410.50110.7216-0.4258-0.08291.7534-0.18730.04261.69680.55022.027-51.490124.787493.7902
20-0.2021-0.2424-0.3750.02530.45650.75030.12260.4705-0.0232-0.2221-0.256-0.68560.29190.14620.00261.19170.2010.43611.3227-0.3432.02249.402833.359745.7227
211.1270.2619-0.9529-0.05520.11131.2289-0.05390.1075-0.1242-0.1031-0.0684-0.14820.3015-0.38220.22481.44950.09530.42411.29790.05010.9753-76.807296.3512114.2558
221.64891.4518-0.84540.4807-1.15620.8473-0.16750.13960.4680.11640.10650.134-0.04610.01120.05980.9108-0.18390.20331.1179-0.14521.486621.7218109.573234.8215
231.4282-0.98370.25750.4689-0.139-0.52490.14580.61561.37830.25220.15210.1051-1.19550.49590.38952.94580.182-1.78311.5574-0.55491.3422-29.7809148.858677.1682
24-0.0443-1.1334-0.13291.83290.5902-0.084-0.81940.4306-0.73930.28550.2670.57910.48690.38590.28061.29920.11020.31561.1794-0.29521.92563.697521.728857.4945
250.7177-0.0626-0.4724-0.04380.74021.1630.24960.02750.13020.0038-0.1404-0.0234-0.1193-0.16760.02231.46270.18060.30251.04340.13121.0003-70.9491112.5646116.6065
261.8696-0.6419-0.00320.6224-0.1871-0.1379-0.09140.76692.92230.1990.7093-0.6065-1.8311-0.51320.43844.28-0.722-2.40671.22110.29330.8171-13.4332151.020771.2643
270.0253-0.0981-0.30050.25570.28480.40570.1599-0.4175-0.44310.34690.14260.61080.6491-0.6163-0.07581.7093-0.25810.15262.01180.58131.8132-59.769832.529107.1531
281.92851.3305-0.7653-0.0296-0.77960.7199-0.32270.1674-0.421-0.2124-0.0178-0.13070.2773-0.15120.28211.0741-0.2630.39560.9576-0.24671.301630.682494.587934.4758
291.55970.78390.10141.9101-1.24590.7985-0.5140.4708-0.9135-1.14950.2385-0.4210.54280.66650.27721.4417-0.01760.45671.10380.03051.5644-37.347-28.8881-34.1811
301.9223-0.0761-0.5141.0745-1.36021.8517-0.20160.8375-0.3216-1.02150.0446-0.4087-0.0470.51380.31021.6254-0.25350.27791.2309-0.01661.4636-38.4619-13.013-41.535
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 340 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 340 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 340 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 340 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 340 )
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 221 )
7X-RAY DIFFRACTION7chain 'G' and (resid 1 through 221 )
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 221 )
9X-RAY DIFFRACTION9chain 'I' and (resid 1 through 221 )
10X-RAY DIFFRACTION10chain 'K' and (resid 1 through 210 )
11X-RAY DIFFRACTION11chain 'L' and (resid 1 through 210 )
12X-RAY DIFFRACTION12chain 'N' and (resid 1 through 210 )
13X-RAY DIFFRACTION13chain 'O' and (resid 1 through 210 )
14X-RAY DIFFRACTION14chain 'P' and (resid 1 through 340 )
15X-RAY DIFFRACTION15chain 'Q' and (resid 1 through 340 )
16X-RAY DIFFRACTION16chain 'R' and (resid 1 through 340 )
17X-RAY DIFFRACTION17chain 'S' and (resid 1 through 340 )
18X-RAY DIFFRACTION18chain 'T' and (resid 1 through 340 )
19X-RAY DIFFRACTION19chain 'U' and (resid 1 through 221 )
20X-RAY DIFFRACTION20chain 'V' and (resid 1 through 221 )
21X-RAY DIFFRACTION21chain 'W' and (resid 1 through 221 )
22X-RAY DIFFRACTION22chain 'X' and (resid 1 through 221 )
23X-RAY DIFFRACTION23chain 'Y' and (resid 1 through 221 )
24X-RAY DIFFRACTION24chain 'Z' and (resid 1 through 210 )
25X-RAY DIFFRACTION25chain 'f' and (resid 1 through 210 )
26X-RAY DIFFRACTION26chain 'g' and (resid 1 through 210 )
27X-RAY DIFFRACTION27chain 'h' and (resid 1 through 210 )
28X-RAY DIFFRACTION28chain 'i' and (resid 1 through 210 )
29X-RAY DIFFRACTION29chain 'J' and (resid 1 through 221 )
30X-RAY DIFFRACTION30chain 'M' and (resid 1 through 210 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more