[English] 日本語
Yorodumi
- PDB-5lgj: THE CRYSTAL STRUCTURE OF IGE FC MUTANT - P333C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lgj
TitleTHE CRYSTAL STRUCTURE OF IGE FC MUTANT - P333C
Components(Ig epsilon chain C ...) x 2
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN DOMAIN / GLYCOPROTEIN
Function / homology
Function and homology information


adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / type I hypersensitivity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / type 2 immune response ...adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / type I hypersensitivity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / type 2 immune response / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / mast cell degranulation / B cell proliferation / macrophage differentiation / Role of LAT2/NTAL/LAB on calcium mobilization / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / complement activation, classical pathway / FCERI mediated MAPK activation / antigen binding / B cell receptor signaling pathway / FCERI mediated NF-kB activation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / inflammatory response / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsDhaliwal, B. / Pang, M.O.Y. / Sutton, B.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
Wellcome Trust United Kingdom
Asthma UK United Kingdom
CitationJournal: To Be Published
Title: THE CRYSTAL STRUCTURE OF IGE FC MUTANT - P333C
Authors: Dhaliwal, B. / Pang, M.O.Y. / Keeble, A.H. / Taylor, A.I. / James, L.K. / Gould, H.J. / McDonnell, J.M. / Beavil, A.J. / Sutton, B.J.
History
DepositionJul 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact ...pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_unobs_or_zero_occ_atoms / struct_asym / struct_conn / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ig epsilon chain C region
B: Ig epsilon chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,13111
Polymers71,1212
Non-polymers3,0119
Water4,234235
1
A: Ig epsilon chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1197
Polymers35,5321
Non-polymers1,5876
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ig epsilon chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0124
Polymers35,5891
Non-polymers1,4233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.450, 74.910, 79.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

-
Ig epsilon chain C ... , 2 types, 2 molecules AB

#1: Protein Ig epsilon chain C region


Mass: 35531.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHE / Production host: Mus musculus (house mouse) / References: UniProt: P01854
#2: Protein Ig epsilon chain C region


Mass: 35588.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHE / Production host: Mus musculus (house mouse) / References: UniProt: P01854

-
Sugars , 2 types, 2 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)]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
DManpa1-3[DManpa1-4]DManpa1-6[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_e4-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]{}[(4+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 242 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 16% w/v PEG 8,000, 0.1M Tris-HCl pH 8.5, 0.2 M lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Apr 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→67.5 Å / Num. obs: 24092 / % possible obs: 99.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 6.8
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.611

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimlessdata scaling
PHASERphasing
BUSTER-TNT2.10.0refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WQR

2wqr


Resolution: 2.6→29.49 Å / Cor.coef. Fo:Fc: 0.9254 / Cor.coef. Fo:Fc free: 0.8728 / SU R Cruickshank DPI: 0.668 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.855 / SU Rfree Blow DPI: 0.305 / SU Rfree Cruickshank DPI: 0.303
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 1223 5.09 %RANDOM
Rwork0.1879 ---
obs0.1909 24044 98.94 %-
Displacement parametersBiso max: 211.02 Å2 / Biso mean: 57.46 Å2 / Biso min: 13.99 Å2
Baniso -1Baniso -2Baniso -3
1-2.1765 Å20 Å20 Å2
2--0.5431 Å20 Å2
3----2.7196 Å2
Refine analyzeLuzzati coordinate error obs: 0.338 Å
Refinement stepCycle: final / Resolution: 2.6→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4875 0 195 235 5305
Biso mean--93.86 42.61 -
Num. residues----624
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1792SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes110HARMONIC2
X-RAY DIFFRACTIONt_gen_planes728HARMONIC5
X-RAY DIFFRACTIONt_it5186HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion743SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5544SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5186HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg7071HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion18.76
LS refinement shellResolution: 2.6→2.71 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2745 142 4.87 %
Rwork0.2276 2772 -
all0.2299 2914 -
obs--98.94 %
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)
18.59541.84736.99772.89083.47519.95610.25990.4116-0.5296-0.3073-0.3359-0.2110.43020.60520.0760.108-0.00110.03640.37180.01320.129223.19099.213454.2513
22.4698-0.74921.10343.2076-0.21624.07090.2914-0.1854-0.3835-0.0872-0.06090.40850.2976-0.132-0.23050.0034-0.048600.07520.03350.127617.660314.78359.0996
30.712-11.5293.833227.3392-3.480300.204-0.14040.2216-2.1841-0.12351.342-0.282-0.6078-0.08051.07980.52030.04460.5911-0.02790.434321.157423.896231.5826
41.0222-4.0665-0.184611.78570.26259.39860.39830.20350.5744-0.66930.1297-1.1624-1.59720.3187-0.52790.372-0.06950.16090.0588-0.16260.427939.974413.053729.309
535.564657.8027-8.827298.6886-20.52373.016-0.55640.3336-2.0853-0.27230.4431-2.3371-0.15070.06130.11330.99360.31990.05730.5001-0.09831.076423.26135.583325.9396
63.87730.43661.89556.16830.55063.110.2730.30971.1688-0.9607-0.0255-0.5069-1.6953-0.0463-0.24761.36120.02830.26810.1080.04440.356435.309627.145231.4017
74.80390.39330.107810.29776.99673.23380.5339-0.28170.4777-0.69090.283-1.388-1.08170.0785-0.8170.57170.02210.25110.0525-0.01480.262538.755317.613134.9356
815.1221-18.25851.520424.6883.78095.2607-0.05830.45240.2682-0.7734-0.50590.4273-1.0586-0.32270.56421.03750.4810.20280.51360.02890.448625.466929.122237.2598
90.78990.47412.64212.6594-0.15580.02290.19910.02740.16610.226-0.02070.03490.290.3052-0.1784-0.0301-0.01450.06210.10330.03390.083534.6118-1.549416.7363
103.4077-0.00291.27031.86090.23841.57090.13780.16080.32590.1273-0.1976-0.1698-0.07930.01050.05980.08230.00380.02960.06820.02440.130139.8859-0.273915.9476
112.3534-2.35890.38975.67982.11383.63330.3747-0.1419-1.40160.1078-0.54591.1721.1923-0.61720.17130.3854-0.1415-0.23230.1414-0.00970.572613.16750.604747.8549
1221.5880.458425.522212.348711.10429.02190.6774-0.7404-0.6804-0.35280.1248-0.12390.5152-0.3302-0.80220.90770.2412-0.16190.2968-0.02410.534820.6093-3.940336.4272
136.4791-4.094-1.17489.03466.00030.7557-0.00910.1646-1.229-0.09090.08970.48480.5846-0.0577-0.08060.38570.2325-0.33410.361-0.15060.267518.48151.529645.2664
145.55982.3531-1.390212.77580.02261.35810.459-0.0756-1.21721.1034-0.87930.40330.3505-0.98620.42030.61810.0188-0.46090.473-0.35220.72859.74460.625840.6827
155.2181-5.9896-8.17233.62077.423915.91330.21370.15880.0438-0.076-0.0785-0.0565-0.2889-0.3959-0.13521.0334-0.0724-0.3370.673-0.08730.79839.673524.823531.9819
166.9221-2.061-0.80335.08370.25150.2192-0.0215-0.67130.27320.0493-0.0382-0.0817-0.0294-0.0050.0597-0.0878-0.0009-0.05970.1685-0.01190.17433.270113.508110.161
175.3725-1.0124.38814.69470.62550.176-0.1984-0.73760.3590.39450.1044-0.615-0.1059-0.65870.094-0.11710.0119-0.08320.272-0.03780.0455-1.912313.093115.2717
182.0694-0.70430.32731.0093-0.70880.68810.0473-0.03080.46520.0792-0.0973-0.0828-0.08040.09090.050.0839-0.0247-0.02740.1226-0.03350.168615.49137.058.7211
192.07620.15090.46062.2805-0.15652.8807-0.08730.27770.30960.20230.09190.0799-0.2755-0.1363-0.00460.00330.02230.04150.18380.02610.081719.4361-0.70279.3681
202.7727-0.05370.49161.655-0.68170.94620.06620.0916-0.2482-0.10810.06180.12420.23250.0019-0.1280.06050.0080.01790.11670.00180.208120.8044-9.83818.0607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|228 - A|244 }A228 - 244
2X-RAY DIFFRACTION2{ A|245 - A|329 }A245 - 329
3X-RAY DIFFRACTION3{ A|334 - A|341 }A334 - 341
4X-RAY DIFFRACTION4{ A|342 - A|362 }A342 - 362
5X-RAY DIFFRACTION5{ A|363 - A|368 }A363 - 368
6X-RAY DIFFRACTION6{ A|369 - A|396 }A369 - 396
7X-RAY DIFFRACTION7{ A|397 - A|417 }A397 - 417
8X-RAY DIFFRACTION8{ A|418 - A|431 }A418 - 431
9X-RAY DIFFRACTION9{ A|432 - A|470 }A432 - 470
10X-RAY DIFFRACTION10{ A|471 - A|545 }A471 - 545
11X-RAY DIFFRACTION11{ B|231 - B|272 }B231 - 272
12X-RAY DIFFRACTION12{ B|273 - B|282 }B273 - 282
13X-RAY DIFFRACTION13{ B|283 - B|309 }B283 - 309
14X-RAY DIFFRACTION14{ B|310 - B|330 }B310 - 330
15X-RAY DIFFRACTION15{ B|331 - B|336 }B331 - 336
16X-RAY DIFFRACTION16{ B|337 - B|380 }B337 - 380
17X-RAY DIFFRACTION17{ B|381 - B|407 }B381 - 407
18X-RAY DIFFRACTION18{ B|408 - B|469 }B408 - 469
19X-RAY DIFFRACTION19{ B|470 - B|502 }B470 - 502
20X-RAY DIFFRACTION20{ B|503 - B|546 }B503 - 546

+
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://pdbjlvh1.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