[English] 日本語
Yorodumi
- PDB-5c0r: Crystal Structure of a Generation 3 Influenza Hemagglutinin Stabi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5c0r
TitleCrystal Structure of a Generation 3 Influenza Hemagglutinin Stabilized Stem Complexed with the Broadly Neutralizing Antibody C179
Components
  • C179 Fab heavy chain
  • C179 Fab light chain
  • Hemagglutinin, Envelope glycoprotein, Fibritin fusion protein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Hemagglutinin / immunogen / trimer / complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / viral budding from plasma membrane ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / viral budding from plasma membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / host cell surface receptor binding / symbiont entry into host cell / apical plasma membrane / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / membrane
Similarity search - Function
Fibritin C-terminal / Fibritin C-terminal region / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like ...Fibritin C-terminal / Fibritin C-terminal region / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibritin / Envelope glycoprotein gp160 / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Human immunodeficiency virus type 1 group M subtype B
Enterobacteria phage T4 (virus)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.188 Å
AuthorsBoyington, J.C. / kwong, P.D. / Nabel, G.J. / Mascola, J.R.
CitationJournal: Nat Med / Year: 2015
Title: Hemagglutinin-stem nanoparticles generate heterosubtypic influenza protection.
Authors: Hadi M Yassine / Jeffrey C Boyington / Patrick M McTamney / Chih-Jen Wei / Masaru Kanekiyo / Wing-Pui Kong / John R Gallagher / Lingshu Wang / Yi Zhang / M Gordon Joyce / Daniel Lingwood / ...Authors: Hadi M Yassine / Jeffrey C Boyington / Patrick M McTamney / Chih-Jen Wei / Masaru Kanekiyo / Wing-Pui Kong / John R Gallagher / Lingshu Wang / Yi Zhang / M Gordon Joyce / Daniel Lingwood / Syed M Moin / Hanne Andersen / Yoshinobu Okuno / Srinivas S Rao / Audray K Harris / Peter D Kwong / John R Mascola / Gary J Nabel / Barney S Graham /
Abstract: The antibody response to influenza is primarily focused on the head region of the hemagglutinin (HA) glycoprotein, which in turn undergoes antigenic drift, thus necessitating annual updates of ...The antibody response to influenza is primarily focused on the head region of the hemagglutinin (HA) glycoprotein, which in turn undergoes antigenic drift, thus necessitating annual updates of influenza vaccines. In contrast, the immunogenically subdominant stem region of HA is highly conserved and recognized by antibodies capable of binding multiple HA subtypes. Here we report the structure-based development of an H1 HA stem-only immunogen that confers heterosubtypic protection in mice and ferrets. Six iterative cycles of structure-based design (Gen1-Gen6) yielded successive H1 HA stabilized-stem (HA-SS) immunogens that lack the immunodominant head domain. Antigenic characterization, determination of two HA-SS crystal structures in complex with stem-specific monoclonal antibodies and cryo-electron microscopy analysis of HA-SS on ferritin nanoparticles (H1-SS-np) confirmed the preservation of key structural elements. Vaccination of mice and ferrets with H1-SS-np elicited broadly cross-reactive antibodies that completely protected mice and partially protected ferrets against lethal heterosubtypic H5N1 influenza virus challenge despite the absence of detectable H5N1 neutralizing activity in vitro. Passive transfer of immunoglobulin from H1-SS-np-immunized mice to naive mice conferred protection against H5N1 challenge, indicating that vaccine-elicited HA stem-specific antibodies can protect against diverse group 1 influenza strains.
History
DepositionJun 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Source and taxonomy
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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_struct_oper_list / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 2.1Sep 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
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
A: Hemagglutinin, Envelope glycoprotein, Fibritin fusion protein
L: C179 Fab light chain
H: C179 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5765
Polymers82,9303
Non-polymers6462
Water1448
1
A: Hemagglutinin, Envelope glycoprotein, Fibritin fusion protein
L: C179 Fab light chain
H: C179 Fab heavy chain
hetero molecules

A: Hemagglutinin, Envelope glycoprotein, Fibritin fusion protein
L: C179 Fab light chain
H: C179 Fab heavy chain
hetero molecules

A: Hemagglutinin, Envelope glycoprotein, Fibritin fusion protein
L: C179 Fab light chain
H: C179 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,72815
Polymers248,7919
Non-polymers1,9376
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area30530 Å2
ΔGint-167 kcal/mol
Surface area95400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.038, 112.038, 205.125
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

-
Antibody , 2 types, 2 molecules LH

#2: Antibody C179 Fab light chain


Mass: 23451.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)
#3: Antibody C179 Fab heavy chain


Mass: 25062.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)

-
Protein / Non-polymers , 2 types, 9 molecules A

#1: Protein Hemagglutinin, Envelope glycoprotein, Fibritin fusion protein


Mass: 34416.082 Da / Num. of mol.: 1
Fragment: UNP Q6WG00 residues 18-49, 328-402, 436-517, UNP P04578 residues 546-577, 628-654 and UNP D9IEJ2 residues 458-485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus, Human immunodeficiency virus type 1 group M subtype B, Enterobacteria phage T4
Strain: A/New Caledonia/20/1999(H1N1), isolate HXB2 / Gene: HA, env, wac / Cell line (production host): HEK293F / Organ (production host): Kidney / Production host: Homo sapiens (human)
References: UniProt: Q6WG00, UniProt: P04578, UniProt: D9IEJ2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

-
Sugars , 2 types, 2 molecules

#4: 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.: 1
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
#5: 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.: 1
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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% (w/v) PEG 1500, 5% (v/v) MPD, 200 mM ammonium chloride, 100 mM Tris, pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2010
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.188→50 Å / Num. obs: 15742 / % possible obs: 98.25 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 94.77 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.2
Reflection shellResolution: 3.188→3.3 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.6 / % possible all: 87.1

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
MOLREPphasing
PHENIX1.8.4_1496refinement
Coot0.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RU7 (5-36, 315-323 chain A, 514-559, 590-660 chain B), 1SZT (3-29, 42-67 chain A), 1Q9K (1-111 chain B), 1UWX (3-108 chain K), 1RFO (1-27, chain A)

1ru7

1szt

1q9k

1uwx

1rfo


Resolution: 3.188→32.343 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 783 4.98 %Random selection
Rwork0.1992 ---
obs0.2018 15733 98.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.188→32.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5499 0 42 8 5549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035672
X-RAY DIFFRACTIONf_angle_d0.6647702
X-RAY DIFFRACTIONf_dihedral_angle_d13.4482032
X-RAY DIFFRACTIONf_chiral_restr0.028857
X-RAY DIFFRACTIONf_plane_restr0.002987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.188-3.38750.38271300.31812283X-RAY DIFFRACTION91
3.3875-3.64870.31591120.26122545X-RAY DIFFRACTION100
3.6487-4.01530.25961510.22922510X-RAY DIFFRACTION100
4.0153-4.59490.24761430.19262534X-RAY DIFFRACTION100
4.5949-5.78370.24421280.18132528X-RAY DIFFRACTION100
5.7837-32.34420.20971190.16582550X-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)
13.8160.75944.31961.48850.45858.2863-0.302-0.23820.43180.5106-0.29830.0543-1.18670.17-0.01871.0283-0.2443-0.05180.8248-0.02620.842718.247511.7465-16.6535
20.1550.60640.94940.96642.18133.9361-0.31810.6680.8352-0.3882-0.697-0.44970.29331.0666-0.62770.8495-0.0957-0.04771.16710.15590.836212.92986.1436-53.0492
31.77740.550.96661.0981.26243.342-0.1069-0.22070.35580.0172-0.36450.1374-0.1566-0.3315-0.01080.742-0.1102-0.07090.6710.09870.84057.07292.7303-37.3824
45.8703-3.51760.01494.51191.36881.8216-0.1215-0.6705-0.91791.7246-0.2831-0.8909-0.63321.5161-1.391.3443-0.3911-0.36811.7140.35741.175127.99950.37780.6069
56.3312-2.2994-6.47335.68623.09596.8836-0.0405-1.1361-1.07051.8105-0.5661-0.37631.43950.0009-0.95591.9083-0.4676-0.4721.95460.10161.108725.8759-3.78312.9941
61.7966-1.90091.06242.096-0.88941.2405-2.1660.5991-1.35290.43982.1909-0.5323-0.6026-1.3972-0.01962.3616-0.41870.05442.1818-0.13321.87153.86895.058610.3274
77.33550.9143-2.37121.05250.27545.99960.1349-1.3314-2.95870.7056-0.5354-0.63160.58391.6495-2.6290.8747-0.1772-0.46751.46940.41211.998252.8688-3.5907-22.1563
85.13053.3712-1.40424.79441.85713.3697-0.0547-1.3189-1.42460.3561-0.0229-1.27050.0930.8672-3.15320.7095-0.1523-0.41051.41320.38031.019345.13072.2017-19.2877
91.13180.363-0.20825.9367-3.28712.8222-0.217-0.2488-2.7221-0.7649-0.11520.27950.9856-0.9293-0.25150.7646-0.1345-0.14490.99080.08361.671339.2347-1.6402-28.9773
106.16330.2034-1.34830.1432-0.50541.305-0.4936-1.2137-2.67770.4157-0.0074-0.76880.32370.4744-0.32420.8987-0.1061-0.14151.15890.33022.164449.4895-4.4897-26.1852
112.9711-2.36781.24353.5895-0.14415.5138-0.01122.713-2.3649-0.33840.77510.25810.3784-0.15140.59770.845-0.1375-0.09392.0146-0.62991.74475.008-3.4745-46.4698
121.4151-0.7809-0.32030.5591-0.42792.30280.44690.8274-2.04270.36470.40510.9196-0.06270.40610.05410.99440.0242-0.07331.2731-0.33112.271.6654-3.7671-40.2937
131.6094-1.5528-0.91121.91852.77059.21680.49010.9322-0.5825-0.9376-0.0857-0.6606-1.25121.4611-0.30460.7384-0.06520.09941.9804-0.62441.589984.25941.3588-47.4259
149.17180.8458-4.20270.60720.33252.91660.2811.0362-3.8337-0.3368-1.02711.29610.46260.36191.91940.95210.06150.211.8185-0.62062.5681.5696-11.2463-41.91
157.22850.9742-3.09797.284-1.55387.74210.31630.3340.7950.086-0.05550.0219-0.9565-0.2355-0.00360.8554-0.0529-0.07310.9060.11481.016941.51317.3885-34.1193
160.2106-0.4719-0.63583.42031.52722.36960.2208-0.05690.76190.8194-0.1055-0.3074-0.9311-0.16070.01991.0167-0.22570.02161.29020.21181.271643.017423.0738-38.0957
176.31980.1836-1.50671.2160.14940.35961.3919-0.60270.47770.0099-0.7336-0.6404-0.2773-0.07380.23740.7811-0.2091-0.05081.26840.21610.96639.907411.5167-32.8092
185.0745-1.33171.68131.68391.03992.16820.70950.3775-0.5033-0.4088-0.3346-0.1623-0.13061.3661-0.00450.813-0.0697-0.17641.2080.01530.977949.45311.8046-40.8348
196.273-2.0375-5.55776.8787-2.15757.4539-0.8593-2.3481-0.7863-1.92060.57760.73762.1158-1.2869-2.32041.7028-0.4566-0.093.1035-1.01262.264977.5735-8.2934-56.3728
202.68542.87590.56213.6559-0.5422.65870.28120.6167-1.5328-0.56671.39760.46070.64340.091713.69710.7764-0.1342-0.25512.3315-0.85422.434565.4197-0.664-53.4743
212.04882.5017-1.49673.9331-0.22224.11410.18452.0852-1.3074-1.31670.30381.71110.6849-0.8892.84270.8665-0.0635-0.41841.9623-0.90282.756762.5745-4.0569-51.0596
220.7277-1.7402-1.95035.42634.04495.89930.07862.4866-2.4021-1.76340.7276-0.45550.20070.29395.09191.32140.0415-0.20582.3627-1.34683.300568.0774-6.5734-55.5375
230.31761.09370.46024.18830.58873.1460.68150.3669-0.9707-0.770.67650.19391.15171.09263.5460.93440.1395-0.43442.6552-0.78751.418965.67650.8751-61.9901
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:85 and not (element H)
2X-RAY DIFFRACTION2chain A and resid 86:145 and not (element H)
3X-RAY DIFFRACTION3chain A and resid 146:214 and not (element H)
4X-RAY DIFFRACTION4chain A and resid 215:242 and not (element H)
5X-RAY DIFFRACTION5chain A and resid 243:255 and not (element H)
6X-RAY DIFFRACTION6chain A and resid 260:285 and not (element H)
7X-RAY DIFFRACTION7chain L and resid 1:18 and not (element H)
8X-RAY DIFFRACTION8chain L and resid 19:38 and not (element H)
9X-RAY DIFFRACTION9chain L and resid 39:58 and not (element H)
10X-RAY DIFFRACTION10chain L and resid 59:116 and not (element H)
11X-RAY DIFFRACTION11chain L and resid 117:148 and not (element H)
12X-RAY DIFFRACTION12chain L and resid 149:175 and not (element H)
13X-RAY DIFFRACTION13chain L and resid 176:197 and not (element H)
14X-RAY DIFFRACTION14chain L and resid 198:212 and not (element H)
15X-RAY DIFFRACTION15chain H and resid 1:69 and not (element H)
16X-RAY DIFFRACTION16chain H and resid 70:85 and not (element H)
17X-RAY DIFFRACTION17chain H and resid 86:99 and not (element H)
18X-RAY DIFFRACTION18chain H and resid 100:120 and not (element H)
19X-RAY DIFFRACTION19chain H and resid 121:132 and not (element H)
20X-RAY DIFFRACTION20chain H and resid 133:154 and not (element H)
21X-RAY DIFFRACTION21chain H and resid 155:171 and not (element H)
22X-RAY DIFFRACTION22chain H and resid 172:193 and not (element H)
23X-RAY DIFFRACTION23chain H and resid 194:213 and not (element H)

+
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