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- PDB-6ieq: Crystal Structure of HIV-1 Env ConM SOSIP.v7 in Complex with bNAb... -

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Basic information

Entry
Database: PDB / ID: 6ieq
TitleCrystal Structure of HIV-1 Env ConM SOSIP.v7 in Complex with bNAb PGT124 and 35O22
Components
  • (Envelope glycoprotein ...) x 2
  • 35O22 Fab Heavy Chain
  • 35O22 Fab Light Chain
  • PGT124 Fab Heavy Chain
  • PGT124 Fab Light Chain
KeywordsVIRAL PROTEIN / HIV-1 / Envelop Protein / Consensus sequence-based ConM SOSIP / broadly neutralizing antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 6alpha-alpha-mannobiose / alpha-D-mannopyranose
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsHan, B.W. / Wilson, I.A.
CitationJournal: Nat Commun / Year: 2019
Title: Structure and immunogenicity of a stabilized HIV-1 envelope trimer based on a group-M consensus sequence.
Authors: Sliepen, K. / Han, B.W. / Bontjer, I. / Mooij, P. / Garces, F. / Behrens, A.J. / Rantalainen, K. / Kumar, S. / Sarkar, A. / Brouwer, P.J.M. / Hua, Y. / Tolazzi, M. / Schermer, E. / Torres, J. ...Authors: Sliepen, K. / Han, B.W. / Bontjer, I. / Mooij, P. / Garces, F. / Behrens, A.J. / Rantalainen, K. / Kumar, S. / Sarkar, A. / Brouwer, P.J.M. / Hua, Y. / Tolazzi, M. / Schermer, E. / Torres, J.L. / Ozorowski, G. / van der Woude, P. / de la Pena, A.T. / van Breemen, M.J. / Camacho-Sanchez, J.M. / Burger, J.A. / Medina-Ramirez, M. / Gonzalez, N. / Alcami, J. / LaBranche, C. / Scarlatti, G. / van Gils, M.J. / Crispin, M. / Montefiori, D.C. / Ward, A.B. / Koopman, G. / Moore, J.P. / Shattock, R.J. / Bogers, W.M. / Wilson, I.A. / Sanders, R.W.
History
DepositionSep 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / entity_src_gen / 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 / 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.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_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 2.1Nov 22, 2023Group: 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
Revision 2.2Mar 20, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
G: Envelope glycoprotein gp160
B: Envelope glycoprotein gp160
L: PGT124 Fab Light Chain
H: PGT124 Fab Heavy Chain
D: 35O22 Fab Heavy Chain
E: 35O22 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,56125
Polymers171,0866
Non-polymers9,47619
Water0
1
G: Envelope glycoprotein gp160
L: PGT124 Fab Light Chain
H: PGT124 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,80320
Polymers104,7693
Non-polymers9,03317
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Envelope glycoprotein gp160
D: 35O22 Fab Heavy Chain
E: 35O22 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7595
Polymers66,3163
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.590, 127.590, 315.507
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Envelope glycoprotein ... , 2 types, 2 molecules GB

#1: Protein Envelope glycoprotein gp160


Mass: 56252.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)
#2: Protein Envelope glycoprotein gp160


Mass: 17214.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)

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Antibody , 4 types, 4 molecules LHDE

#3: Antibody PGT124 Fab Light Chain


Mass: 23056.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody PGT124 Fab Heavy Chain


Mass: 25460.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody 35O22 Fab Heavy Chain


Mass: 25783.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Antibody 35O22 Fab Light Chain


Mass: 23318.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 8 types, 19 molecules

#7: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 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]{}}}}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#9: 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.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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
#10: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-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: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#11: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose / 6alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-6DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#12: 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-(1-6)-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: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-6DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g6-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#13: 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.: 7
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
#14: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Sequence detailsAuthors follow residue numbers from HBx numbering, which specifies residue number according to the ...Authors follow residue numbers from HBx numbering, which specifies residue number according to the sequence alignment results with HBx standard. So, those three sequence number gaps come from three short deletions of our ConM SOSIP.v7 sequence. UNK reisues in the sample sequence were just added for the HBx numbering. They are non-entity.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.05 Å3/Da / Density % sol: 69.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 3.93
Details: 0.07 M sodium acetate, 30% (v/v) glycerol, 6% (w/v) PEG 4000, pH 3.93
PH range: 3.93 - 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03315 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 23583 / % possible obs: 89 % / Redundancy: 17.5 % / CC1/2: 0.95 / Rpim(I) all: 0.04 / Rsym value: 0.15 / Net I/σ(I): 15.7
Reflection shellResolution: 3.9→4.04 Å / Redundancy: 12.3 % / Num. unique obs: 1613 / CC1/2: 0.7 / Rpim(I) all: 0.28 / Rsym value: 1.07 / % possible all: 61.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CEZ
Resolution: 3.9→50.01 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / Cross valid method: THROUGHOUT / ESU R Free: 0.89 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29605 1193 5.1 %RANDOM
Rwork0.24742 ---
obs0.24979 22323 88.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 247.532 Å2
Baniso -1Baniso -2Baniso -3
1-8.64 Å24.32 Å20 Å2
2--8.64 Å20 Å2
3----28.01 Å2
Refinement stepCycle: 1 / Resolution: 3.9→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11221 0 625 0 11846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212166
X-RAY DIFFRACTIONr_bond_other_d00.0210768
X-RAY DIFFRACTIONr_angle_refined_deg1.322.00416637
X-RAY DIFFRACTIONr_angle_other_deg3.825325251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7351439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35824.501471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.227151866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3441551
X-RAY DIFFRACTIONr_chiral_restr0.1320.22002
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02112853
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022295
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_it7.61425.5045798
X-RAY DIFFRACTIONr_mcbond_other7.61425.5025797
X-RAY DIFFRACTIONr_mcangle_it12.93838.2437223
X-RAY DIFFRACTIONr_mcangle_other12.93738.2457224
X-RAY DIFFRACTIONr_scbond_it6.43925.7396368
X-RAY DIFFRACTIONr_scbond_other6.43725.7376366
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.38238.5449414
X-RAY DIFFRACTIONr_long_range_B_refined18.46412511
X-RAY DIFFRACTIONr_long_range_B_other18.46312512
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.9→4.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 56 -
Rwork0.454 1136 -
obs--60.69 %

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