[English] 日本語
Yorodumi
- PDB-2wqz: Crystal structure of synaptic protein neuroligin-4 in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wqz
TitleCrystal structure of synaptic protein neuroligin-4 in complex with neurexin-beta 1: alternative refinement
Components
  • NEUREXIN-1-BETA
  • NEUROLIGIN 4, X-LINKED
KeywordsCELL ADHESION / TRANSMEMBRANE / DISULFIDE BOND / ALPHA/BETA-HYDROLASE CHOLINESTERASE AUTISM BRAIN / ALTERNATIVE PROMOTER USAGE / MEMBRANE / GLYCOPROTEIN
Function / homology
Function and homology information


asymmetric, glutamatergic, excitatory synapse / protein-containing complex assembly involved in synapse maturation / positive regulation of cAMP-mediated signaling / positive regulation of presynaptic active zone assembly / cell-cell adhesion involved in synapse maturation / guanylate kinase-associated protein clustering / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / neuron to neuron synapse / trans-synaptic protein complex ...asymmetric, glutamatergic, excitatory synapse / protein-containing complex assembly involved in synapse maturation / positive regulation of cAMP-mediated signaling / positive regulation of presynaptic active zone assembly / cell-cell adhesion involved in synapse maturation / guanylate kinase-associated protein clustering / protein complex involved in cell-cell adhesion / positive regulation of neuromuscular synaptic transmission / neuron to neuron synapse / trans-synaptic protein complex / neuroligin clustering involved in postsynaptic membrane assembly / symmetric, GABA-ergic, inhibitory synapse / regulation of trans-synaptic signaling by endocannabinoid, modulating synaptic transmission / type 1 fibroblast growth factor receptor binding / trans-synaptic signaling, modulating synaptic transmission / cerebellar granule cell differentiation / negative regulation of filopodium assembly / gephyrin clustering involved in postsynaptic density assembly / slit diaphragm / postsynaptic density protein 95 clustering / postsynaptic membrane assembly / synapse maturation / gamma-aminobutyric acid receptor clustering / vocal learning / presynaptic membrane assembly / neuroligin family protein binding / neurexin family protein binding / positive regulation of synapse maturation / maintenance of synapse structure / regulation of grooming behavior / presynapse assembly / synaptic vesicle clustering / brainstem development / synaptic membrane adhesion / regulation of postsynaptic specialization assembly / positive regulation of fibroblast growth factor receptor signaling pathway / receptor localization to synapse / neuron cell-cell adhesion / inhibitory synapse / NMDA glutamate receptor clustering / negative regulation of excitatory postsynaptic potential / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / vocalization behavior / regulation of postsynaptic density assembly / protein localization to synapse / acetylcholine receptor binding / cell-cell junction organization / neurotransmitter secretion / regulation of synaptic vesicle cycle / AMPA selective glutamate receptor signaling pathway / positive regulation of synapse assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / NMDA selective glutamate receptor signaling pathway / Neurexins and neuroligins / chloride ion binding / organ growth / neuromuscular process controlling balance / postsynaptic specialization membrane / regulation of synapse assembly / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / adult behavior / neuron projection morphogenesis / excitatory synapse / social behavior / endocytic vesicle / regulation of presynapse assembly / positive regulation of excitatory postsynaptic potential / positive regulation of synaptic transmission, glutamatergic / prepulse inhibition / axonal growth cone / cell adhesion molecule binding / synapse assembly / presynaptic active zone membrane / cellular response to calcium ion / cerebellum development / positive regulation of synaptic transmission, GABAergic / learning / calcium channel regulator activity / positive regulation of protein localization to plasma membrane / neuromuscular junction / establishment of protein localization / synapse organization / postsynaptic density membrane / positive regulation of neuron projection development / circadian rhythm / modulation of chemical synaptic transmission / GABA-ergic synapse / Schaffer collateral - CA1 synapse / neuron differentiation / neuron projection development / calcium-dependent protein binding / transmembrane signaling receptor activity / presynaptic membrane / scaffold protein binding / vesicle / angiogenesis / nuclear membrane / chemical synaptic transmission / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
Similarity search - Function
Syndecan/Neurexin domain / Syndecan domain / Neuroligin / : / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / Laminin G domain / Laminin G domain profile. / Laminin G domain ...Syndecan/Neurexin domain / Syndecan domain / Neuroligin / : / Neurexin/syndecan/glycophorin C / putative band 4.1 homologues' binding motif / : / Laminin G domain / Laminin G domain profile. / Laminin G domain / Laminin G domain / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Jelly Rolls - #200 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Neurexin-1-beta / Neuroligin-4, X-linked
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
RATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsFabrichny, I.P. / Leone, P. / Sulzenbacher, G. / Comoletti, D. / Miller, M.T. / Taylor, P. / Bourne, Y. / Marchot, P.
CitationJournal: Neuron / Year: 2007
Title: Structural Analysis of the Synaptic Protein Neuroligin and its Beta-Neurexin Complex: Determinants for Folding and Cell Adhesion.
Authors: Fabrichny, I.P. / Leone, P. / Sulzenbacher, G. / Comoletti, D. / Miller, M.T. / Taylor, P. / Bourne, Y. / Marchot, P.
History
DepositionAug 28, 2009Deposition site: PDBE / Processing site: PDBE
SupersessionSep 8, 2009ID: 2VH8
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 24, 2016Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Source and taxonomy
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 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 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NEUROLIGIN 4, X-LINKED
B: NEUROLIGIN 4, X-LINKED
C: NEUREXIN-1-BETA
D: NEUREXIN-1-BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,7188
Polymers171,1964
Non-polymers5234
Water00
1
A: NEUROLIGIN 4, X-LINKED
D: NEUREXIN-1-BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0805
Polymers85,5982
Non-polymers4823
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: NEUROLIGIN 4, X-LINKED
C: NEUREXIN-1-BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6383
Polymers85,5982
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)158.520, 198.670, 85.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALALEULEU4AA41 - 6210 - 31
211ALAALALEULEU4BB41 - 6210 - 31
121PROPROCYSCYS4AA69 - 11038 - 79
221PROPROCYSCYS4BB69 - 11038 - 79
131ASNASNTYRTYR4AA143 - 407112 - 376
231ASNASNTYRTYR4BB143 - 407112 - 376
141ASPASPHISHIS4AA414 - 598383 - 567
241ASPASPHISHIS4BB414 - 598383 - 567
112HISHISVALVAL6CC82 - 2883 - 179
212HISHISVALVAL6DD82 - 2883 - 179

NCS ensembles :
ID
1
2

-
Components

#1: Protein NEUROLIGIN 4, X-LINKED / NEUROLIGIN X / HNLX / NEUROLIGIN 4


Mass: 66230.203 Da / Num. of mol.: 2 / Fragment: ACETYLCHOLINESTERASE-LIKE DOMAIN, RESIDUES 43-619
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCDNA3 / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q8N0W4
#2: Protein NEUREXIN-1-BETA / NEUREXIN I-BETA / BETA-NEUREXIN 1


Mass: 19367.713 Da / Num. of mol.: 2 / Fragment: LNS DOMAIN, RESIDUES 80-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (BL21(DE3) (bacteria) / Variant (production host): ROSETTA / References: UniProt: Q63373
#3: 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.: 2
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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.24 Å3/Da / Density % sol: 70.8 % / Description: NONE
Crystal growpH: 6.5 / Details: 8% PEG 20000, 0.1M MES PH6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.9→30 Å / Num. obs: 25251 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.1
Reflection shellResolution: 3.9→4 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3BE8 AND 1C4R

3be8

1c4r


Resolution: 3.9→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.886 / SU B: 107.112 / SU ML: 0.634 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0 / ESU R Free: 0.754 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1261 5 %RANDOM
Rwork0.205 ---
obs0.208 23955 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.99 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å20 Å20 Å2
2--1.97 Å20 Å2
3----4.42 Å2
Refinement stepCycle: LAST / Resolution: 3.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11330 0 30 0 11360
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02211652
X-RAY DIFFRACTIONr_bond_other_d0.0030.027685
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.94815870
X-RAY DIFFRACTIONr_angle_other_deg0.964318751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.92151434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61824.595555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.169151825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8431554
X-RAY DIFFRACTIONr_chiral_restr0.0810.21728
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113088
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022340
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_it0.2651.57162
X-RAY DIFFRACTIONr_mcbond_other0.0311.52926
X-RAY DIFFRACTIONr_mcangle_it0.505211575
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.51834490
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.9354.54295
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A6558medium positional0.580.5
12B6558medium positional0.580.5
21C2284loose positional0.695
22D2284loose positional0.695
11A6558medium thermal0.192
12B6558medium thermal0.192
21C2284loose thermal2.4210
22D2284loose thermal2.4210
LS refinement shellResolution: 3.9→4 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 90 -
Rwork0.351 1708 -
obs--100 %
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)
13.40870.566-0.19844.75590.64532.7718-0.1461-0.122-0.2798-0.1501-0.00440.24690.67320.45920.15050.74290.34620.02740.9095-0.04790.134216.921-27.962-22.967
21.60480.6614.97441.28143.377517.4789-0.0338-0.183-0.18681.29820.4799-0.01281.42670.7992-0.4461.81880.34430.04021.66650.24180.717824.317-28.193-3.251
32.50740.01031.034214.431.77921.6264-0.2819-0.7186-0.64030.57850.8047-0.91520.46110.3944-0.52281.11280.6648-0.18941.5468-0.00020.649641.916-35.176-12.789
42.386-0.3204-1.422710.65771.55347.58020.1149-0.50920.2596-0.03850.0884-1.2435-0.23730.9898-0.20340.52790.0308-0.02571.3331-0.17380.221133.13-1.957-8.574
52.89714.0361-1.26657.25141.58287.88240.205-0.50950.2750.6509-0.68140.74350.2661-0.20730.47640.67230.3120.05830.9139-0.08780.45868.222-15.334-11.919
63.12431.15670.50524.891-0.26952.6647-0.41550.61571.0476-0.30230.18840.1987-0.6450.36130.22720.9559-0.32830.00011.07020.31630.703735.9744.926-9.784
711.61485.82678.56143.47456.16213.3244-0.1439-0.20840.7209-0.5226-0.11150.2169-0.70350.47660.25542.1428-0.10760.43521.76740.51331.173137.77842.657-30.574
84.673-2.2472-4.04411.50792.24783.7246-0.38630.33450.2952-0.08380.6924-0.56260.17710.26-0.30611.3321-0.61160.40932.21850.30291.190558.32441.003-26.196
92.3971.79121.8228.5945-0.80286.9745-0.04921.1385-0.1969-0.78620.079-0.72920.09250.9092-0.02981.0246-0.20060.29111.58310.00420.25735.45115.232-25.278
101.7031-2.7991.52925.8026-1.58183.26430.1520.6180.1203-0.9769-0.50670.7353-0.86610.35370.35481.1597-0.3895-0.12811.29440.48850.99720.1737.877-17.834
118.64910.1871-1.03853.88311.4078.01250.1207-0.29550.03030.85910.0575-0.08840.0819-0.5901-0.17821.0191-0.17760.18930.6880.27320.577144.82234.74524.502
123.49262.33211.16262.4429-0.24218.4211-0.23061.3767-0.2489-0.91790.22820.15690.4506-0.13250.00241.59710.4487-0.11521.7505-0.15230.463422.314-18.18-58.799
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 110
2X-RAY DIFFRACTION1A143 - 291
3X-RAY DIFFRACTION1A340 - 373
4X-RAY DIFFRACTION1A449 - 472
5X-RAY DIFFRACTION1A561 - 582
6X-RAY DIFFRACTION2A111 - 142
7X-RAY DIFFRACTION3A292 - 339
8X-RAY DIFFRACTION4A374 - 448
9X-RAY DIFFRACTION4A583 - 598
10X-RAY DIFFRACTION5A473 - 560
11X-RAY DIFFRACTION6B41 - 110
12X-RAY DIFFRACTION6B143 - 291
13X-RAY DIFFRACTION6B340 - 373
14X-RAY DIFFRACTION6B449 - 472
15X-RAY DIFFRACTION6B561 - 582
16X-RAY DIFFRACTION7B111 - 142
17X-RAY DIFFRACTION8B292 - 339
18X-RAY DIFFRACTION9B374 - 448
19X-RAY DIFFRACTION9B583 - 599
20X-RAY DIFFRACTION10B473 - 560
21X-RAY DIFFRACTION11C82 - 288
22X-RAY DIFFRACTION12D82 - 288

+
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