[English] 日本語
Yorodumi
- PDB-4nco: Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nco
TitleCrystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with the Broadly Neutralizing Fab PGT122
Components
  • BG505 SOSIP gp120
  • BG505 SOSIP gp41
  • PGT122 heavy chain
  • PGT122 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Type-1 membrane fusion glycoprotein trimer / HIV-1 envelope / gp120 / gp41 / membrane fusion / viral entry / CD4 / CCR5/CXCR4 / broadly neutralizing antibodies / viral surface / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
2alpha-alpha-mannobiose / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.7 Å
AuthorsJulien, J.-P. / Stanfield, R.L. / Lyumkis, D. / Ward, A.B. / Wilson, I.A.
CitationJournal: Science / Year: 2013
Title: Crystal structure of a soluble cleaved HIV-1 envelope trimer.
Authors: Julien, J.P. / Cupo, A. / Sok, D. / Stanfield, R.L. / Lyumkis, D. / Deller, M.C. / Klasse, P.J. / Burton, D.R. / Sanders, R.W. / Moore, J.P. / Ward, A.B. / Wilson, I.A.
History
DepositionOct 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _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
Revision 2.1Sep 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
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: BG505 SOSIP gp120
B: BG505 SOSIP gp41
C: PGT122 light chain
D: PGT122 heavy chain
E: BG505 SOSIP gp120
F: BG505 SOSIP gp41
G: PGT122 light chain
H: PGT122 heavy chain
I: BG505 SOSIP gp120
J: BG505 SOSIP gp41
K: PGT122 light chain
L: PGT122 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)350,93560
Polymers323,77212
Non-polymers27,16348
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.200, 260.720, 283.180
Angle α, β, γ (deg.)90.00, 99.56, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 2 types, 6 molecules AEIBFJ

#1: Protein BG505 SOSIP gp120


Mass: 53121.105 Da / Num. of mol.: 3 / Fragment: UNP residues 30-504 / Mutation: T332N,A501C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#2: Protein BG505 SOSIP gp41


Mass: 6656.196 Da / Num. of mol.: 3 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell line (production host): HEK / Production host: Homo sapiens (human)

-
Antibody , 2 types, 6 molecules CGKDHL

#3: Antibody PGT122 light chain


Mass: 22712.082 Da / Num. of mol.: 3 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human)
#4: Antibody PGT122 heavy chain


Mass: 25434.691 Da / Num. of mol.: 3 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human)

-
Sugars , 4 types, 48 molecules

#5: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.: 12
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]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_e6-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]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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: 1559.386 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_h2-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#8: 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.: 30
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

-
Details

Sequence detailsTHE SEQUENCE OF CHAINS B, F, AND J IS ...THE SEQUENCE OF CHAINS B, F, AND J IS AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD (CONTAINS I559P AND T605C MUTATIONS) BUT ALL RESIDUES ARE MODELED AS ALANINE AND REPORTED AS "UNKNOWN RESIDUE."

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 8.56 Å3/Da / Density % sol: 85.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.1 M CAPS, 2 M ammonium sulfate, 0.2 M lithium sulfate, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2013
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 4.7→40 Å / Num. all: 51575 / Num. obs: 51575 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.3 / Net I/σ(I): 4.9
Reflection shellResolution: 4.7→4.8 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2 / Num. unique all: 2040 / % possible all: 59.4

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4JY5 AND 3JWD, EMDB ENTRY EMD-5624

4jy5

3jwd


Resolution: 4.7→39.892 Å / SU ML: 1.04 / σ(F): 1.43 / Phase error: 48.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3893 2547 5.06 %RANDOM
Rwork0.3752 ---
obs0.3759 50320 88.99 %-
all-51575 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.7→39.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20217 0 1797 0 22014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622644
X-RAY DIFFRACTIONf_angle_d1.38931071
X-RAY DIFFRACTIONf_dihedral_angle_d28.7828439
X-RAY DIFFRACTIONf_chiral_restr0.0693963
X-RAY DIFFRACTIONf_plane_restr0.0073711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.7-4.79030.50091000.40821755X-RAY DIFFRACTION60
4.7903-4.88790.4301990.40761909X-RAY DIFFRACTION64
4.8879-4.9940.43431340.38582095X-RAY DIFFRACTION72
4.994-5.10990.40871230.38362303X-RAY DIFFRACTION78
5.1099-5.23740.38751310.39032484X-RAY DIFFRACTION83
5.2374-5.37870.43561290.37372527X-RAY DIFFRACTION85
5.3787-5.53660.37561260.36682591X-RAY DIFFRACTION87
5.5366-5.71480.36031340.37562677X-RAY DIFFRACTION90
5.7148-5.91840.40981530.38232739X-RAY DIFFRACTION92
5.9184-6.15460.40751480.38572829X-RAY DIFFRACTION95
6.1546-6.43360.41811620.39342959X-RAY DIFFRACTION99
6.4336-6.77120.43351400.39622986X-RAY DIFFRACTION100
6.7712-7.19320.40611600.39742983X-RAY DIFFRACTION100
7.1932-7.74480.39111570.39432956X-RAY DIFFRACTION100
7.7448-8.51740.411790.3722973X-RAY DIFFRACTION100
8.5174-9.73420.34561480.33582991X-RAY DIFFRACTION100
9.7342-12.20550.35231680.31532976X-RAY DIFFRACTION100
12.2055-39.89340.37161560.41093040X-RAY DIFFRACTION99
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)
1-0.10360.09440.0972-0.0956-0.0033-0.03231.19980.59042.2206-0.5340.3426-0.0979-0.49990.10630-1.26211.5182-1.72171.2877-0.5129-0.5054192.0521-3.226358.1657
20.00720.05520.07220.08090.01650.02750.2046-0.1023-0.1825-0.0335-0.07310.23460.30310.000700.84820.1581-0.75481.07670.62980.396192.5071-23.6259390.549
3-0.2474-0.211-0.1992-0.1724-0.0056-0.0740.46240.68820.9394-0.09190.7292-0.8486-0.56350.64790-1.686-0.17651.7103-0.5114-0.9232-2.9825155.207916.8909324.7262
4-0.0194-0.02810.0066-0.01950.00360.0016-0.0281-0.2446-0.19650.25240.1275-0.210.20620.158200.2332-0.00010.83590.0154-0.37570.3413125.277812.1693318.1002
5-0.00860.0338-0.0182-0.0655-0.01130.0060.0097-0.04150.04120.00880.0067-0.3896-0.05870.06440-0.0437-0.02890.53170.20780.0774-1.1886115.486430.5343291.4901
6-0.0567-0.156-0.05370.1223-0.01-0.0971-0.55320.3848-1.1907-1.9414-0.0899-1.59950.75190.3830-0.5090.27880.9382-0.14092.7843-2.2239104.7719-22.1778392.2057
7-0.00250.0266-0.1298-0.11060.0005-0.0071-0.33540.152-0.85920.2377-0.13261.84430.0072-0.695300.3659-0.5898-1.6197-0.1082-1.4626-0.369133.222268.6058380.6325
8-0.0005-0.04290.05520.03460.00640.03090.0230.00740.04440.351-0.1377-0.13570.13760.0745-00.5481-0.39410.87510.9924-0.5132-0.5936102.3799-2.7074425.0748
90.0161-0.0089-0.0299-0.0111-0.0040.0104-0.23690.25770.2002-0.1544-0.0917-0.1316-0.21540.06601.6392-0.7345-0.94061.64071.34312.4293165.197870.2911401.8105
10-0.30170.1288-0.1361-0.57610.2247-0.13860.29440.1391-0.3184-0.5439-0.00920.43281.1378-0.1596-0-2.5457-0.10612.3265-0.76091.3591-3.0278115.769-13.7703340.252
11-0.1284-0.11050.1838-0.1244-0.1056-0.27140.23530.34820.178-0.08370.32720.447-0.5341-0.37860-1.207-1.1166-1.2593-1.5235-1.3552-1.0328111.096138.7613341.8391
12-0.03860.0391-0.0141-0.08890.0378-0.00860.0891-0.13840.00560.2213-0.02020.1221-0.02250.00290-0.5819-0.594-0.1207-0.1660.06470.7858117.680610.1087320.9838
13-0.0255-0.0140.0512-0.0050.0153-0.03040.0479-0.04740.02870.1912-0.0951-0.1575-0.13010.099100.78440.74880.06210.23890.40821.0479120.04818.9247319.9039
14-0.04340.04970.0106-0.00320.03730.013-0.1849-0.08950.18140.0792-0.1735-0.11360.0803-0.0414-00.4515-0.43320.57630.5476-0.4439-0.1162122.5602-0.3136288.7981
150.0205-0.00920.00670.0075-0.03810.01960.07470.0950.0684-0.13550.06450.01330.181-0.0122-00.328-0.0267-0.15310.1133-0.02580.163194.48829.878299.3891
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1((chain 'C' and resid 8 through 109) or (chain 'D' and resid 1 through 109))
2X-RAY DIFFRACTION2((chain 'C' and resid 110 through 209) or (chain 'D' and resid 110 through 211))
3X-RAY DIFFRACTION3(chain 'A' and resid 44 through 493)
4X-RAY DIFFRACTION4(chain 'B' and resid 1 through 37)
5X-RAY DIFFRACTION5(chain 'B' and resid 101 through 140)
6X-RAY DIFFRACTION6((chain 'G' and resid 8 through 109) or (chain 'H' and resid 1 through 109))
7X-RAY DIFFRACTION7((chain 'K' and resid 8 through 109) or (chain 'L' and resid 1 through 109))
8X-RAY DIFFRACTION8((chain 'G' and resid 110 through 209) or (chain 'H' and resid 110 through 211))
9X-RAY DIFFRACTION9((chain 'K' and resid 110 through 209) or (chain 'L' and resid 110 through 211))
10X-RAY DIFFRACTION10(chain 'E' and resid 44 through 493)
11X-RAY DIFFRACTION11(chain 'I' and resid 44 through 493)
12X-RAY DIFFRACTION12(chain 'F' and resid 1 through 37)
13X-RAY DIFFRACTION13(chain 'J' and resid 1 through 37)
14X-RAY DIFFRACTION14(chain 'F' and resid 101 through 140)
15X-RAY DIFFRACTION15(chain 'J' and resid 101 through 140)

+
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