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- PDB-5vli: Computationally designed inhibitor peptide HB1.6928.2.3 in comple... -

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Basic information

Entry
Database: PDB / ID: 5vli
TitleComputationally designed inhibitor peptide HB1.6928.2.3 in complex with influenza hemagglutinin (A/PuertoRico/8/1934)
Components
  • (Hemagglutinin) x 2
  • Computationally designed peptide HB1.6928.2.3
KeywordsVIRAL PROTEIN/DE NOVO PROTEIN / inhibitor / protein design / influenza / hemagglutinin / VIRAL PROTEIN-DE NOVO PROTEIN complex
Function / homology
Function and homology information


Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation ...Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation / viral budding from plasma membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 / extracellular region / plasma membrane
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 2,5,8,11-TETRAOXATRIDECANE / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsBernard, S.M. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56AI117675 United States
CitationJournal: Nature / Year: 2017
Title: Massively parallel de novo protein design for targeted therapeutics.
Authors: Chevalier, A. / Silva, D.A. / Rocklin, G.J. / Hicks, D.R. / Vergara, R. / Murapa, P. / Bernard, S.M. / Zhang, L. / Lam, K.H. / Yao, G. / Bahl, C.D. / Miyashita, S.I. / Goreshnik, I. / ...Authors: Chevalier, A. / Silva, D.A. / Rocklin, G.J. / Hicks, D.R. / Vergara, R. / Murapa, P. / Bernard, S.M. / Zhang, L. / Lam, K.H. / Yao, G. / Bahl, C.D. / Miyashita, S.I. / Goreshnik, I. / Fuller, J.T. / Koday, M.T. / Jenkins, C.M. / Colvin, T. / Carter, L. / Bohn, A. / Bryan, C.M. / Fernandez-Velasco, D.A. / Stewart, L. / Dong, M. / Huang, X. / Jin, R. / Wilson, I.A. / Fuller, D.H. / Baker, D.
History
DepositionApr 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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_special_symmetry / 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_struct_special_symmetry.label_asym_id / _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 2.1Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Computationally designed peptide HB1.6928.2.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,14810
Polymers61,4053
Non-polymers1,7437
Water7,566420
1
A: Hemagglutinin
B: Hemagglutinin
C: Computationally designed peptide HB1.6928.2.3
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
C: Computationally designed peptide HB1.6928.2.3
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
C: Computationally designed peptide HB1.6928.2.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,44330
Polymers184,2159
Non-polymers5,22821
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 area32550 Å2
ΔGint-204 kcal/mol
Surface area64590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.649, 110.649, 327.378
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-917-

HOH

21B-946-

HOH

31B-976-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Hemagglutinin /


Mass: 36721.367 Da / Num. of mol.: 1 / Fragment: 17-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
Strain: A/Puerto Rico/8/1934 H1N1 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03452
#2: Protein Hemagglutinin /


Mass: 20138.393 Da / Num. of mol.: 1 / Fragment: UNP residues 344-519
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Puerto Rico/8/1934 H1N1)
Strain: A/Puerto Rico/8/1934 H1N1 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03452

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Computationally designed peptide HB1.6928.2.3


Mass: 4545.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 3 types, 3 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: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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.: 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

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Non-polymers , 3 types, 424 molecules

#7: Chemical ChemComp-PGF / 2,5,8,11-TETRAOXATRIDECANE


Mass: 192.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O4
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C4H10O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O

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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: 3.14 Å3/Da / Density % sol: 60.83 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 5% PEG 3000, 30% PEG 200, 100 mM MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976484 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976484 Å / Relative weight: 1
ReflectionResolution: 1.799→50 Å / Num. obs: 71757 / % possible obs: 100 % / Redundancy: 16.1 % / CC1/2: 0.973 / Rpim(I) all: 0.023 / Rsym value: 0.089 / Net I/σ(I): 27
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.87 / Rpim(I) all: 0.47 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RVX
Resolution: 1.799→49.345 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2128 3578 4.99 %
Rwork0.182 --
obs0.1835 71713 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.799→49.345 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4220 0 115 420 4755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184466
X-RAY DIFFRACTIONf_angle_d1.4546052
X-RAY DIFFRACTIONf_dihedral_angle_d15.8232662
X-RAY DIFFRACTIONf_chiral_restr0.1658
X-RAY DIFFRACTIONf_plane_restr0.01777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7987-1.82240.31771400.27722549X-RAY DIFFRACTION98
1.8224-1.84730.28281430.26762597X-RAY DIFFRACTION100
1.8473-1.87370.27351360.25082575X-RAY DIFFRACTION100
1.8737-1.90170.32051440.25912593X-RAY DIFFRACTION100
1.9017-1.93140.36541360.29592579X-RAY DIFFRACTION99
1.9314-1.96310.3171440.23942565X-RAY DIFFRACTION100
1.9631-1.99690.23311180.22892634X-RAY DIFFRACTION100
1.9969-2.03330.27731340.2122615X-RAY DIFFRACTION100
2.0333-2.07240.24621550.20232583X-RAY DIFFRACTION100
2.0724-2.11470.25061300.20262596X-RAY DIFFRACTION100
2.1147-2.16060.23121370.19292608X-RAY DIFFRACTION100
2.1606-2.21090.22621230.17442642X-RAY DIFFRACTION100
2.2109-2.26620.2351270.21812594X-RAY DIFFRACTION99
2.2662-2.32750.27031340.19942591X-RAY DIFFRACTION99
2.3275-2.3960.25551260.18992651X-RAY DIFFRACTION100
2.396-2.47330.28691110.18352632X-RAY DIFFRACTION100
2.4733-2.56170.20811530.18922588X-RAY DIFFRACTION100
2.5617-2.66420.21911460.17922605X-RAY DIFFRACTION100
2.6642-2.78550.20421420.18482622X-RAY DIFFRACTION100
2.7855-2.93230.21911270.17792646X-RAY DIFFRACTION99
2.9323-3.1160.20581630.17712606X-RAY DIFFRACTION100
3.116-3.35660.20271410.17562652X-RAY DIFFRACTION100
3.3566-3.69420.19731250.16082658X-RAY DIFFRACTION100
3.6942-4.22850.16831560.15272654X-RAY DIFFRACTION100
4.2285-5.32650.16071420.14552686X-RAY DIFFRACTION100
5.3265-49.36380.20911450.19282814X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.5901-0.0944-0.5860.41170.67394.3890.00530.08210.0497-0.11940.0444-0.1324-0.19070.2529-0.06110.2301-0.03620.02960.24760.03970.325223.24391.619863.3352
21.3667-0.36950.40472.2339-0.36332.0308-0.07510.8738-0.3021-0.5718-0.096-0.42910.05120.60130.18540.3988-0.02010.12920.6873-0.05820.381425.0616-7.039730.8463
32.20850.4864-0.87963.5457-0.05884.15760.11441.2424-0.1375-0.6376-0.0693-0.2556-0.03280.2601-0.00490.51250.03630.10360.9108-0.10560.358318.8861-7.903721.1479
42.8677-0.0820.49122.90741.12893.60680.04940.9351-0.0496-0.5853-0.17430.1436-0.0483-0.12290.13770.34330.02990.08880.5715-0.04260.280814.9043-5.745428.6084
50.2609-0.1592-0.850.31370.58146.2309-0.0647-0.03190.0413-0.0576-0.0383-0.1343-0.12060.15360.09050.1841-0.02690.01410.19580.03240.274521.15931.488970.9744
64.0779-0.75943.37652.0922-0.84575.6682-0.0857-0.26590.14280.15160.0172-0.2691-0.16290.34270.07770.19570.0023-0.02640.3089-0.01610.245218.96460.8678108.8571
74.89781.53393.97072.02661.933.49150.04140.0105-0.09860.1073-0.0161-0.06860.54430.0013-0.0330.19610.0186-0.00190.21640.02130.341813.7915-9.223790.5775
85.3019-1.1404-0.33966.1746-1.35839.2125-0.2640.0447-0.00870.17750.51030.59350.1027-0.4468-0.25470.2174-0.03370.01490.39030.05930.34813.8181-4.357562.9558
95.1991-5.34555.57465.4899-5.70576.02340.29841.11210.3483-0.3527-0.6013-0.51170.04620.84320.35210.31570.03920.0450.38120.04890.28727.06426.121543.1365
100.8672-0.38972.23730.3075-0.87139.7214-0.0241-0.1951-0.03490.05760.14380.0085-0.202-0.4261-0.10590.16790.00990.00510.22750.01740.25366.40591.413486.1873
113.1781-2.07172.46885.6571-5.45648.2605-0.3077-0.76580.1790.82250.26250.0555-0.9192-0.11510.07130.3730.12-0.04070.6304-0.0480.272515.6211-0.2247122.2912
122.97661.1235-0.73535.43481.90146.1309-0.129-0.5002-0.299-00.321-0.04790.7527-0.1942-0.23630.34250.0986-0.05490.51210.07240.304717.9319-11.2074118.2903
133.291.36430.82034.36194.83696.2706-0.2287-1.4598-0.50741.04770.0392-0.01580.8557-0.42720.0280.55770.0605-0.02481.23170.16210.263611.5498-8.2592130.8212
145.2193-1.10985.73582.5208-0.03589.35630.45370.406-0.61710.0513-0.00710.06450.98870.4445-0.37980.29460.0623-0.02840.3482-0.00320.384723.5193-11.653789.0193
153.38410.09722.76828.6197-2.02553.35320.69990.9136-1.8021-0.57690.06580.74841.88720.7658-0.8240.51360.1127-0.16010.4736-0.16330.742223.5016-18.41386.1361
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 101 )
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 150 )
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 195 )
4X-RAY DIFFRACTION4chain 'A' and (resid 196 through 270 )
5X-RAY DIFFRACTION5chain 'A' and (resid 271 through 325 )
6X-RAY DIFFRACTION6chain 'B' and (resid 501 through 537 )
7X-RAY DIFFRACTION7chain 'B' and (resid 538 through 558 )
8X-RAY DIFFRACTION8chain 'B' and (resid 559 through 568 )
9X-RAY DIFFRACTION9chain 'B' and (resid 569 through 574 )
10X-RAY DIFFRACTION10chain 'B' and (resid 575 through 632 )
11X-RAY DIFFRACTION11chain 'B' and (resid 633 through 645 )
12X-RAY DIFFRACTION12chain 'B' and (resid 646 through 658 )
13X-RAY DIFFRACTION13chain 'B' and (resid 659 through 669 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 29 )
15X-RAY DIFFRACTION15chain 'C' and (resid 30 through 40 )

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