[English] 日本語
Yorodumi
- PDB-3saj: Crystal Structure of glutamate receptor GluA1 Amino Terminal Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3saj
TitleCrystal Structure of glutamate receptor GluA1 Amino Terminal Domain
ComponentsGlutamate receptor 1
KeywordsTRANSPORT PROTEIN / Rossmann fold / ion channel / membrane
Function / homology
Function and homology information


Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / chemical synaptic transmission, postsynaptic / COPII-mediated vesicle transport / positive regulation of membrane potential / cellular response to ammonium ion / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / neuron spine / myosin V binding ...Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / chemical synaptic transmission, postsynaptic / COPII-mediated vesicle transport / positive regulation of membrane potential / cellular response to ammonium ion / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / neuron spine / myosin V binding / Trafficking of AMPA receptors / dendritic spine membrane / response to arsenic-containing substance / cellular response to dsRNA / Synaptic adhesion-like molecules / long-term synaptic depression / beta-2 adrenergic receptor binding / protein kinase A binding / cellular response to peptide hormone stimulus / neuronal cell body membrane / spinal cord development / Activation of AMPA receptors / response to lithium ion / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding / AMPA glutamate receptor complex / neuronal action potential / excitatory synapse / ionotropic glutamate receptor complex / adenylate cyclase binding / cellular response to organic cyclic compound / asymmetric synapse / G-protein alpha-subunit binding / regulation of postsynaptic membrane potential / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / glutamate receptor binding / positive regulation of synaptic transmission / response to electrical stimulus / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / synapse assembly / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / monoatomic ion transmembrane transport / dendritic shaft / response to cocaine / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / cellular response to amino acid stimulus / postsynaptic density membrane / regulation of synaptic plasticity / modulation of chemical synaptic transmission / neuromuscular junction / receptor internalization / synaptic vesicle membrane / response to organic cyclic compound / cerebral cortex development / response to peptide hormone / response to toxic substance / cellular response to growth factor stimulus / recycling endosome / small GTPase binding / recycling endosome membrane / G-protein beta-subunit binding / cell-cell junction / synaptic vesicle / presynapse / response to estradiol / presynaptic membrane / cell body / amyloid-beta binding / chemical synaptic transmission / postsynaptic membrane / early endosome membrane / postsynapse / scaffold protein binding / dendritic spine / postsynaptic density / early endosome / neuron projection / response to xenobiotic stimulus / protein domain specific binding / dendrite / neuronal cell body / glutamatergic synapse / synapse / endoplasmic reticulum membrane / positive regulation of gene expression / protein kinase binding / cell surface / endoplasmic reticulum
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Response regulator / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Response regulator / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamate receptor 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJin, R. / Zong, Y. / Yao, G. / Gu, S.
CitationJournal: Biochem.J. / Year: 2011
Title: Crystal structure of the glutamate receptor GluA1 N-terminal domain.
Authors: Yao, G. / Zong, Y. / Gu, S. / Zhou, J. / Xu, H. / Mathews, I.I. / Jin, R.
History
DepositionJun 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate receptor 1
B: Glutamate receptor 1
C: Glutamate receptor 1
D: Glutamate receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,90619
Polymers176,8534
Non-polymers7,05415
Water2,576143
1
A: Glutamate receptor 1
C: Glutamate receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1679
Polymers88,4262
Non-polymers3,7407
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint50 kcal/mol
Surface area34110 Å2
MethodPISA
2
B: Glutamate receptor 1
D: Glutamate receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,74010
Polymers88,4262
Non-polymers3,3138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint40 kcal/mol
Surface area34160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.586, 94.421, 186.367
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Non-polymers , 2 types, 147 molecules ABCD

#1: Protein
Glutamate receptor 1 / / GluA1 / GluR-1 / AMPA-selective glutamate receptor 1 / GluR-A / GluR-K1 / Glutamate receptor ...GluA1 / GluR-1 / AMPA-selective glutamate receptor 1 / GluR-A / GluR-K1 / Glutamate receptor ionotropic / AMPA 1


Mass: 44213.219 Da / Num. of mol.: 4 / Fragment: N-terminal domain (UNP residues 22-392) / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P19490
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

-
Sugars , 4 types, 15 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_f2-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 5
Details: 22% PEG3350, 0.2 M magnesium chloride, 0.1 M sodium acetate, pH 5.0, EVAPORATION, temperature 290K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 3, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→93.184 Å / Num. obs: 57222 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 10.3
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2255 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→93.18 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.893 / SU B: 23.93 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 0.991 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28569 2886 5.1 %RANDOM
Rwork0.21815 ---
obs0.2216 54093 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.79 Å20 Å20 Å2
2---0.57 Å20 Å2
3---2.36 Å2
Refinement stepCycle: LAST / Resolution: 2.5→93.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11914 0 466 143 12523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02212694
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7911.98617212
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.49351471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.75823.921630
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.776152116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6331598
X-RAY DIFFRACTIONr_chiral_restr0.1110.21952
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219574
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3551.57333
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.138211858
X-RAY DIFFRACTIONr_scbond_it6.13835361
X-RAY DIFFRACTIONr_scangle_it8.1144.55350
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.498→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 211 -
Rwork0.238 3828 -
obs--96.47 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.0134-0.8736-0.15141.7453-0.02092.0231-0.0025-0.081-0.0851-0.00070.03690.12030.012-0.0576-0.03450.1984-0.0065-0.01250.22110.00530.3181-1.5829-5.7382-5.2243
24.03452.3415-1.24593.5908-0.05521.3680.04890.10940.2473-0.55720.0993-0.3465-0.01860.1814-0.14820.34660.08020.08070.256-0.00780.29192.288919.8491-20.0067
38.0904-1.86-0.826125.81299.14357.6388-0.6557-1.30251.7966-0.21931.7018-1.9711-1.48231.446-1.04610.5334-0.11940.32660.4525-0.34320.932910.153732.6226-11.6647
45.1201-1.4834-0.20275.36032.46163.9583-0.1478-0.44910.13010.11250.15340.01150.1180.0771-0.00560.26280.04990.05570.1622-0.05870.3186-2.204326.624-6.1652
53.2427-0.1426-0.47452.3841-0.03981.193-0.073-0.1353-0.23520.20680.10160.6986-0.0487-0.2664-0.02870.18220.0103-0.00590.26160.05660.3786-12.2083-3.0114-7.0553
61.8329-1.05410.11735.2966-0.85810.93980.18810.08850.1086-0.52-0.12860.4837-0.1593-0.1765-0.05950.23290.0294-0.08030.2215-0.0180.3087-11.27377.6184-18.1423
72.76680.2713-0.07822.40490.24321.5829-0.0997-0.0154-0.0617-0.01260.113-0.1614-0.00810.1023-0.01330.2062-0.0024-0.01110.2274-0.00550.320252.2701-33.1199-17.4841
85.88160.3620.40125.8141-1.28623.0765-0.46290.4991-0.608-0.70040.63320.31970.08140.1246-0.17030.3223-0.21260.02670.2228-0.11540.20246.052-49.6342-43.3386
92.73250.91982.03091.04851.46663.96040.08240.2874-0.9186-0.17030.4892-0.95140.76220.6754-0.57160.4124-0.02140.2890.3029-0.33530.894163.5695-50.9214-34.5767
103.86781.33280.40283.5202-0.32771.8075-0.1713-0.17710.01810.29670.2361-0.59640.00890.2176-0.06490.2204-0.003-0.02980.3813-0.0390.389163.7344-29.982-18.6994
117.958-1.7916-2.83112.8921.64482.9772-0.0017-0.19960.4467-0.23890.1798-0.1463-0.32490.28-0.17810.2139-0.0428-0.06560.1899-0.01110.332252.9608-20.899-19.2066
124.48470.5794-0.2650.90870.63565.2353-0.38260.8555-0.6988-0.64280.5177-0.34850.20280.5195-0.13510.4703-0.29780.23130.5348-0.26720.334763.0033-38.6381-40.6487
132.826-0.0948-0.14621.8973-0.18262.1860.0610.0157-0.125-0.0564-0.0014-0.15130.020.1666-0.05950.21330.0012-0.02290.2545-0.0130.334528.6874-7.4735-9.7908
146.078-3.3783.43256.0599-3.5673.3063-0.17050.08040.79580.382-0.0384-0.21-0.5748-0.13860.20880.2786-0.00250.07880.13490.00190.307522.696620.3237-19.121
1514.31813.72971.276417.1155-5.435120.64360.26040.73912.149-1.5471-0.97210.9602-1.1059-1.35040.71170.41130.94190.43861.15810.58640.485416.467424.0014-35.5839
168.1655-5.24421.53544.4524-2.59542.91710.67191.5257-0.0822-0.5632-1.0377-0.34050.10920.78140.36580.21830.01960.17680.4756-0.0080.351436.05128.6644-29.0107
174.12850.1028-1.64540.5719-0.38493.1187-0.0279-0.6276-0.56660.182-0.0671-0.22960.06660.59760.0950.15790.0073-0.0370.24170.03420.416134.5906-7.3215-2.9514
182.50070.21830.77764.3555-1.92972.2695-0.04170.21720.57030.0604-0.1265-0.3917-0.58230.56290.16820.3417-0.1495-0.03390.3528-0.0080.436837.127911.0453-9.6989
192.96540.0427-0.01121.926-0.53472.3252-0.0785-0.00620.1315-0.07380.11410.20830.0112-0.1604-0.03560.1764-0.0048-0.03690.23660.03420.348221.7188-29.3403-18.3188
202.3702-0.0516-1.89530.38191.33516.2315-0.48730.5236-0.3368-0.0820.1130.11351.3488-0.30020.37440.7299-0.2799-0.09080.32840.01430.335322.086-42.926-41.821
215.69790.05980.61454.2451-1.71115.4795-0.31060.2710.0952-0.37230.109-0.12130.3601-0.20520.20160.3549-0.1275-0.03180.2674-0.01860.228732.1404-37.1464-49.6236
224.6166-0.5759-4.38780.56510.78797.6190.05150.71980.5323-0.41220.25070.2349-0.3918-0.8974-0.30220.3613-0.2482-0.30030.44370.20160.334314.6169-28.7716-44.5974
234.77870.2987-1.16292.6084-0.56262.5537-0.2798-0.44290.23460.07570.29840.35480.0305-0.7423-0.01860.19690.0118-0.03780.36680.02250.453512.7711-32.4693-16.1705
241.94220.6079-0.46051.0997-0.30922.6626-0.25120.3583-0.3186-0.56220.37440.26360.6033-0.6852-0.12310.428-0.2093-0.11180.34010.05350.422914.1328-42.1304-30.1555
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 104
2X-RAY DIFFRACTION2A105 - 150
3X-RAY DIFFRACTION3A151 - 178
4X-RAY DIFFRACTION4A179 - 232
5X-RAY DIFFRACTION5A233 - 310
6X-RAY DIFFRACTION6A311 - 372
7X-RAY DIFFRACTION7B2 - 108
8X-RAY DIFFRACTION8B109 - 200
9X-RAY DIFFRACTION9B201 - 255
10X-RAY DIFFRACTION10B256 - 298
11X-RAY DIFFRACTION11B299 - 328
12X-RAY DIFFRACTION12B329 - 371
13X-RAY DIFFRACTION13C2 - 103
14X-RAY DIFFRACTION14C104 - 157
15X-RAY DIFFRACTION15C158 - 178
16X-RAY DIFFRACTION16C179 - 265
17X-RAY DIFFRACTION17C266 - 308
18X-RAY DIFFRACTION18C309 - 371
19X-RAY DIFFRACTION19D1 - 102
20X-RAY DIFFRACTION20D103 - 129
21X-RAY DIFFRACTION21D130 - 179
22X-RAY DIFFRACTION22D180 - 255
23X-RAY DIFFRACTION23D256 - 304
24X-RAY DIFFRACTION24D305 - 371

+
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