[English] 日本語
Yorodumi
- PDB-6gh8: Crystal structure of GP1 domain of Lujo virus in complex with the... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gh8
TitleCrystal structure of GP1 domain of Lujo virus in complex with the first CUB domain of neuropilin-2
Components
  • Glycoprotein
  • Neuropilin-2Neuropilin
KeywordsVIRAL PROTEIN / Viral Glycoprotein / receptor recognition
Function / homology
Function and homology information


vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus ...vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / axon extension involved in axon guidance / NrCAM interactions / sympathetic neuron projection extension / Neurophilin interactions with VEGF and VEGFR / sympathetic ganglion development / neural crest cell migration involved in autonomic nervous system development / vascular endothelial growth factor receptor activity / nerve development / semaphorin receptor complex / outflow tract septum morphogenesis / semaphorin receptor activity / regulation of postsynapse organization / negative chemotaxis / cytokine binding / growth factor binding / semaphorin-plexin signaling pathway / positive regulation of endothelial cell proliferation / cellular response to leukemia inhibitory factor / positive regulation of endothelial cell migration / axon guidance / signaling receptor activity / heparin binding / host cell Golgi apparatus / postsynaptic membrane / angiogenesis / membrane => GO:0016020 / cell adhesion / axon / viral envelope / glutamatergic synapse / extracellular region / membrane / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Spermadhesin, CUB domain / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / Arenavirus glycoprotein, zinc binding domain / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / Arenavirus glycoprotein / Arenavirus glycoprotein / MAM domain, meprin/A5/mu / MAM domain ...Spermadhesin, CUB domain / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / Arenavirus glycoprotein, zinc binding domain / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / Arenavirus glycoprotein / Arenavirus glycoprotein / MAM domain, meprin/A5/mu / MAM domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / MAM domain profile. / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Spermadhesin, CUB domain superfamily / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Glycoprotein / Neuropilin-2
Similarity search - Component
Biological speciesLujo mammarenavirus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsCohen-Dvashi, H. / Kilimnik, I. / Diskin, R.
CitationJournal: Nat Microbiol / Year: 2018
Title: Structural basis for receptor recognition by Lujo virus.
Authors: Cohen-Dvashi, H. / Kilimnik, I. / Diskin, R.
History
DepositionMay 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 17, 2024Group: 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Glycoprotein
A: Neuropilin-2
B: Glycoprotein
C: Neuropilin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6179
Polymers61,8734
Non-polymers7445
Water73941
1
D: Glycoprotein
A: Neuropilin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1984
Polymers30,9362
Non-polymers2612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycoprotein
C: Neuropilin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4195
Polymers30,9362
Non-polymers4823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.808, 59.294, 83.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Glycoprotein /


Mass: 16021.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lujo mammarenavirus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: C5ILC1
#2: Protein Neuropilin-2 / Neuropilin / Vascular endothelial cell growth factor 165 receptor 2


Mass: 14914.466 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRP2, VEGF165R2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O60462
#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 / 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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 0.03M glycyl-glycyl-glycine, 25.9% PEG 6000, 0.09M Bis-Tris Propane pH 9.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.44→72.08 Å / Num. obs: 27109 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.996 / Rrim(I) all: 0.166 / Net I/σ(I): 6
Reflection shellResolution: 2.44→2.5 Å / Redundancy: 4.9 % / CC1/2: 0.497 / Rrim(I) all: 1.241 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(dev_2871: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2qqk

2qqk


Resolution: 2.44→71.996 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 40.13
RfactorNum. reflection% reflection
Rfree0.3115 1339 4.96 %
Rwork0.2656 --
obs0.2679 26973 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.44→71.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3716 0 44 41 3801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043865
X-RAY DIFFRACTIONf_angle_d0.8725242
X-RAY DIFFRACTIONf_dihedral_angle_d24.9841446
X-RAY DIFFRACTIONf_chiral_restr0.053561
X-RAY DIFFRACTIONf_plane_restr0.005688
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4326-2.51950.471190.44632392X-RAY DIFFRACTION94
2.5195-2.62040.41251150.40052551X-RAY DIFFRACTION100
2.6204-2.73960.4211270.37342560X-RAY DIFFRACTION100
2.7396-2.88410.40681200.3532551X-RAY DIFFRACTION100
2.8841-3.06480.36051420.33062521X-RAY DIFFRACTION99
3.0648-3.30140.36721550.32852549X-RAY DIFFRACTION99
3.3014-3.63370.30661330.25532564X-RAY DIFFRACTION100
3.6337-4.15940.29311370.23442573X-RAY DIFFRACTION100
4.1594-5.24020.23271420.19162613X-RAY DIFFRACTION100
5.2402-72.02750.28751490.22532760X-RAY DIFFRACTION100
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)
16.97383.2308-4.44916.3631-1.74664.33820.2159-1.2248-0.7084-0.5986-0.6681-0.90011.48222.11340.85571.57660.184-0.26051.05640.10440.856194.4857-8.901370.3715
23.5988-4.92814.22346.9815-5.89094.9934-0.35990.3611-1.46481.07030.734-1.3913-0.77751.3259-1.09140.8620.0752-0.13070.5559-0.19730.944992.3598-5.987360.8504
34.7823.89671.71773.77283.46687.82520.402-0.7285-0.1966-1.618-0.1837-3.0525-0.15580.1596-0.44190.56130.12930.14630.53730.01530.818596.0565-10.517847.0788
46.53351.16194.17136.24644.80638.41161.0071-0.8375-0.59211.79430.6986-1.16232.40570.1791-1.45541.17160.277-0.10710.64260.03031.001497.792-23.460954.7538
52.4083-0.5051.82184.31784.22316.8687-0.6701-0.7855-1.52851.66431.0415-0.03792.23650.3355-0.48261.28570.1559-0.03880.61210.13010.50688.3647-19.797960.6167
65.2639-4.83162.2894.4347-2.37099.5440.5460.3895-0.6410.4856-0.5377-0.33210.4381-0.94020.18780.9205-0.11050.02320.419-0.1230.73182.3974-14.559547.9804
74.1223-2.56595.47444.2013-2.55647.5421-0.1175-0.23160.21830.80750.3055-0.7493-0.38750.8781-0.15740.72480.0491-0.11830.69010.03150.947699.7627-14.199253.3715
84.7557-4.93395.61595.3018-6.07137.5912-0.38580.4068-0.04070.6173-0.3429-0.73180.97180.67940.7580.77540.10530.07970.38520.04490.790990.8828-10.357752.838
93.5204-3.13322.58396.4078-1.2642.49330.0179-0.7114-0.78680.81050.25340.51521.0125-0.699-0.28260.64150.0740.09670.48280.00210.518278.9623-8.541956.007
104.83751.1744.90828.526-7.0032.0060.1319-1.24030.74010.24240.85860.8609-0.3975-1.19790.73431.08570.06990.16340.5094-0.34360.134982.7674-1.695258.1768
116.82030.8115-1.8778.3577-3.94234.40080.6835-0.6392-1.23210.19570.17240.2599-0.41941.051-0.34751.18960.0765-0.09240.34150.02040.61793.2904-6.767656.5867
127.6092-2.1999-4.42282.48411.41872.5754-1.63232.4886-3.1926-0.4317-0.1610.4578-0.8941.53981.82711.5315-0.3080.14361.3552-0.65031.1342100.3216-7.66470.1054
132.8637-0.4918-1.14453.45970.55384.3702-0.11680.59930.1058-1.1827-0.29410.0806-0.0153-0.27960.39361.0321-0.15480.00450.4245-0.16470.847679.0159-26.148718.7525
142.54-0.61251.75996.7008-1.73322.77430.32340.37060.1351-1.2065-0.20350.5170.28490.2228-0.10830.8195-0.01560.02820.4299-0.20070.67981.5336-21.216122.7129
153.566-1.13380.41087.23612.59637.7726-0.11880.16630.1415-0.77110.3302-0.59450.6420.5777-0.10220.6487-0.0510.10390.2655-0.06070.446687.7631-15.816929.9377
162.8824-0.13012.16216.8241-0.80637.1236-0.45170.4185-0.058-0.5890.1407-0.5762-0.29410.3850.52330.4821-0.13820.03890.3115-0.09230.487385.6982-15.950727.6603
174.029-3.92092.8787.3861-5.26483.73980.34040.6336-0.7462-0.34050.29691.3819-0.70410.0236-0.44981.0438-0.0414-0.02570.5071-0.16060.70274.7773-14.971416.4178
182.0865-1.4651-0.96664.7745-3.30454.64591.107-0.1869-0.322-0.698-0.33641.07132.0360.5632-0.08642.2065-0.1341-0.36441.0453-0.20040.873821.53723.743483.32
192.91851.60111.25071.46252.0793.9017-0.1031-0.06460.18461.4550.3179-0.20540.17550.34740.99311.9610.4891-0.48770.7041-0.30730.894720.962325.771374.4514
202.83971.47751.17264.5568-2.35124.62420.0477-0.6171.4418-0.47750.86121.11210.09210.4856-1.11891.10510.1348-0.11310.6711-0.07281.081824.560322.075359.7905
217.89363.0616-0.68992.9215-2.3474.8184-0.1923-1.36071.08272.11231.49870.77531.02510.4893-1.41921.38590.5982-0.20750.9695-0.01120.698525.70999.136567.6748
223.3083.42.64398.9792-3.06969.12310.68090.0285-0.4232.32160.40930.32211.87630.6114-0.44081.95650.0143-0.08420.6045-0.15790.511916.113812.714272.9667
237.6097-3.26522.7486.6404-1.09484.6022-0.2579-0.29871.0530.6580.292-1.13570.09460.2632-0.08621.21820.1712-0.12050.5173-0.14370.682518.516420.067363.6133
244.34910.09331.59373.88331.09473.6618-0.6379-0.72260.47730.8769-0.05480.4844-0.6556-0.6640.75641.63480.06130.0660.5459-0.06410.84567.059723.670170.0997
256.6902-3.24422.02949.2328-4.02271.8397-0.0986-0.56580.49380.84260.81340.11481.1119-0.0664-0.43891.45770.2016-0.09580.5792-0.28870.527415.949428.453769.8998
265.5521-1.1024-4.35634.5363.38685.29930.00920.0113-2.6101-1.35150.56120.87481.60840.9884-0.311.8871-0.2448-0.27561.2788-0.75531.614828.028624.712382.7778
273.7629-4.0548-0.0476.7428-3.4396.744-1.0272-0.83610.97822.6722-0.241-0.58490.12251.15110.13561.01590.1337-0.02520.46820.11260.710314.2267-1.115836.5264
288.7133-2.7503-0.62819.0176-2.76577.823-0.29690.74520.0256-1.79420.2740.57740.238-0.30440.10910.4483-0.1186-0.09230.2366-0.03320.44597.28459.395828.2223
293.81644.8811-1.16848.2352-4.52995.0110.41350.4030.31610.95640.89920.33580.61050.109-0.73650.44280.1397-0.3080.4124-0.11510.524310.8256.785246.7382
309.0958-1.30530.50089.3255-5.21519.14370.22920.5418-0.1376-0.0171-0.4768-0.34550.06850.381-0.09540.7522-0.0304-0.12840.2625-0.02410.535115.01348.831331.3129
318.8466-0.9327-3.03141.99056.62916.92810.53471.3163-0.5288-2.86550.38510.0964-0.6502-0.8813-0.75490.92070.0048-0.18380.55980.06820.61199.987917.851223.8253
329.0921-4.26722.08954.79-1.45386.2477-0.5695-0.76881.24150.78140.5828-0.5876-0.52590.01830.13350.46390.115-0.0910.3430.00160.574814.42317.331348.591
334.9286-4.70440.19184.7221-1.33716.0065-0.12230.8660.4935-0.1547-0.4027-1.50862.07921.680.48050.80320.1270.09980.6301-0.01190.611321.419215.648532.554
345.73013.4869-2.85728.3016-3.78893.43350.8082-0.13010.7551-0.84550.40731.22770.9010.5189-1.40750.94440.0135-0.03960.3304-0.00530.719719.796221.306836.8434
353.0754-0.84661.36125.9368-2.4982.9079-0.24850.4433-0.0748-0.59280.1637-0.4598-0.03580.07020.04830.6196-0.2301-0.02980.2552-0.14290.299513.777618.695535.2866
362.2015-1.5209-0.12435.1001-0.1663.27820.07850.10290.2367-0.04930.12340.0903-0.08220.3072-0.2330.5118-0.0813-0.050.2557-0.07260.45810.252913.702640.1416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 87 through 95 )
2X-RAY DIFFRACTION2chain 'D' and (resid 96 through 102 )
3X-RAY DIFFRACTION3chain 'D' and (resid 103 through 112 )
4X-RAY DIFFRACTION4chain 'D' and (resid 113 through 120 )
5X-RAY DIFFRACTION5chain 'D' and (resid 121 through 133 )
6X-RAY DIFFRACTION6chain 'D' and (resid 134 through 142 )
7X-RAY DIFFRACTION7chain 'D' and (resid 143 through 151 )
8X-RAY DIFFRACTION8chain 'D' and (resid 152 through 159 )
9X-RAY DIFFRACTION9chain 'D' and (resid 160 through 173 )
10X-RAY DIFFRACTION10chain 'D' and (resid 174 through 182 )
11X-RAY DIFFRACTION11chain 'D' and (resid 183 through 190 )
12X-RAY DIFFRACTION12chain 'D' and (resid 191 through 196 )
13X-RAY DIFFRACTION13chain 'A' and (resid 24 through 41 )
14X-RAY DIFFRACTION14chain 'A' and (resid 42 through 72 )
15X-RAY DIFFRACTION15chain 'A' and (resid 73 through 98 )
16X-RAY DIFFRACTION16chain 'A' and (resid 99 through 135 )
17X-RAY DIFFRACTION17chain 'A' and (resid 136 through 143 )
18X-RAY DIFFRACTION18chain 'B' and (resid 87 through 94 )
19X-RAY DIFFRACTION19chain 'B' and (resid 95 through 102 )
20X-RAY DIFFRACTION20chain 'B' and (resid 103 through 112 )
21X-RAY DIFFRACTION21chain 'B' and (resid 113 through 120 )
22X-RAY DIFFRACTION22chain 'B' and (resid 121 through 133 )
23X-RAY DIFFRACTION23chain 'B' and (resid 134 through 161 )
24X-RAY DIFFRACTION24chain 'B' and (resid 162 through 173 )
25X-RAY DIFFRACTION25chain 'B' and (resid 174 through 190 )
26X-RAY DIFFRACTION26chain 'B' and (resid 191 through 196 )
27X-RAY DIFFRACTION27chain 'C' and (resid 24 through 29 )
28X-RAY DIFFRACTION28chain 'C' and (resid 30 through 41 )
29X-RAY DIFFRACTION29chain 'C' and (resid 42 through 54 )
30X-RAY DIFFRACTION30chain 'C' and (resid 55 through 60 )
31X-RAY DIFFRACTION31chain 'C' and (resid 61 through 72 )
32X-RAY DIFFRACTION32chain 'C' and (resid 73 through 87 )
33X-RAY DIFFRACTION33chain 'C' and (resid 88 through 98 )
34X-RAY DIFFRACTION34chain 'C' and (resid 99 through 104 )
35X-RAY DIFFRACTION35chain 'C' and (resid 105 through 124 )
36X-RAY DIFFRACTION36chain 'C' and (resid 125 through 143 )

+
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