[English] 日本語
Yorodumi
- PDB-4p26: Structure of the P domain from a GI.7 Norovirus variant in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p26
TitleStructure of the P domain from a GI.7 Norovirus variant in complex with A-type 2 HBGA
ComponentsP domain of VP1
KeywordsVIRAL PROTEIN / P domain / Capsid protein / Norovirus / HBGA / A type 2 / Type 2 HBGA / Secretor
Function / homology
Function and homology information


Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Blood group A H type 2 antigen, beta anomer / Major capsid protein
Similarity search - Component
Biological speciesNorovirus Hu/GI.7/TCH-060/USA/2003
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShanker, S. / Czako, R. / Sankaran, B. / Atmar, R. / Estes, M. / Prasad, B.V.V.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Virol. / Year: 2014
Title: Structural analysis of determinants of histo-blood group antigen binding specificity in genogroup I noroviruses.
Authors: Shanker, S. / Czako, R. / Sankaran, B. / Atmar, R.L. / Estes, M.K. / Prasad, B.V.
History
DepositionMar 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 2.0Nov 27, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site_gen
Item: _atom_site.label_asym_id / _atom_site.label_entity_id ..._atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.type / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site_gen.label_asym_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_validate_symm_contact / refine_hist / 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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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.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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Aug 5, 2020Group: Derived calculations / Structure summary / Category: pdbx_molecule_features / struct_conn / Item: _struct_conn.pdbx_leaving_atom_flag
Revision 3.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: P domain of VP1
B: P domain of VP1
C: P domain of VP1
D: P domain of VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,6687
Polymers130,4704
Non-polymers2,1983
Water17,529973
1
A: P domain of VP1
B: P domain of VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7004
Polymers65,2352
Non-polymers1,4652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint17 kcal/mol
Surface area22830 Å2
MethodPISA
2
C: P domain of VP1
D: P domain of VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9683
Polymers65,2352
Non-polymers7331
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-1 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.580, 63.260, 90.430
Angle α, β, γ (deg.)99.25, 97.82, 119.62
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
P domain of VP1


Mass: 32617.451 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GI.7/TCH-060/USA/2003 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G8FL04
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D- ...alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 732.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Blood group A H type 2 antigen, beta anomer
DescriptorTypeProgram
LFucpa1-2[DGalpNAca1-3]DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3-4/a4-b1_b2-c1_b3-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 973 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium Formate 0.1M Bis Tris Propane 20% PEG3350

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.9→34.024 Å / Num. obs: 87902 / % possible obs: 96.8 % / Redundancy: 3.4 % / Net I/σ(I): 9.1

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4P12

4p12


Resolution: 1.9→34.024 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 18.48 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.189 4403 5.01 %Random
Rwork0.1597 ---
obs0.1612 87893 96.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→34.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8743 0 150 973 9866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019151
X-RAY DIFFRACTIONf_angle_d1.31512541
X-RAY DIFFRACTIONf_dihedral_angle_d12.5633326
X-RAY DIFFRACTIONf_chiral_restr0.0851419
X-RAY DIFFRACTIONf_plane_restr0.0061645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.24961500.19312776X-RAY DIFFRACTION95
1.9216-1.94420.24191320.18682723X-RAY DIFFRACTION95
1.9442-1.96790.23031730.18232736X-RAY DIFFRACTION96
1.9679-1.99280.22071400.17862736X-RAY DIFFRACTION96
1.9928-2.0190.24981570.17642772X-RAY DIFFRACTION96
2.019-2.04670.23311400.17722781X-RAY DIFFRACTION96
2.0467-2.07590.22971220.17512764X-RAY DIFFRACTION96
2.0759-2.10690.22321570.17142774X-RAY DIFFRACTION96
2.1069-2.13980.18361380.16832735X-RAY DIFFRACTION96
2.1398-2.17490.20591300.1612777X-RAY DIFFRACTION96
2.1749-2.21240.21031410.1632760X-RAY DIFFRACTION97
2.2124-2.25260.20271450.16292793X-RAY DIFFRACTION96
2.2526-2.2960.19071420.16982741X-RAY DIFFRACTION97
2.296-2.34280.19171580.16782853X-RAY DIFFRACTION97
2.3428-2.39370.22571400.16932721X-RAY DIFFRACTION97
2.3937-2.44940.22931530.16932801X-RAY DIFFRACTION97
2.4494-2.51060.21821720.17322774X-RAY DIFFRACTION97
2.5106-2.57850.20721440.17352743X-RAY DIFFRACTION97
2.5785-2.65430.22341440.16892828X-RAY DIFFRACTION97
2.6543-2.740.20421350.17332818X-RAY DIFFRACTION97
2.74-2.83790.20431320.16552772X-RAY DIFFRACTION97
2.8379-2.95140.21231580.16672781X-RAY DIFFRACTION98
2.9514-3.08570.20751360.16592821X-RAY DIFFRACTION97
3.0857-3.24820.18161480.14972807X-RAY DIFFRACTION98
3.2482-3.45160.16481540.14372800X-RAY DIFFRACTION98
3.4516-3.71780.16411660.14482827X-RAY DIFFRACTION98
3.7178-4.09130.13581650.13692781X-RAY DIFFRACTION98
4.0913-4.6820.1231550.12222799X-RAY DIFFRACTION98
4.682-5.89390.15891310.14352851X-RAY DIFFRACTION98
5.8939-34.02950.1881450.1772845X-RAY DIFFRACTION98
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)
12.6657-0.07120.38582.465-0.07891.6320.03670.08090.13480.0161-0.06740.1208-0.2153-0.0197-0.00160.1149-0.02130.01450.10440.02340.079218.736227.360257.9715
22.266-0.3468-0.38381.02290.0941.2111-0.002-0.32580.02160.15530.0097-0.08490.03320.1911-0.00460.1502-0.0169-0.01980.13290.01170.062430.922418.15467.7657
31.9902-0.0766-0.21111.49360.09022.1541-0.0069-0.1774-0.17660.0663-0.0241-0.18370.13550.23650.00890.08660.0217-0.02520.11210.02410.116839.99059.983960.059
41.8273-0.3327-0.98451.30370.24690.6812-0.0552-0.1823-0.14220.15060.03460.02190.05560.10220.03350.1158-0.0122-0.00060.10740.02130.08920.156413.371265.786
53.25420.46540.06491.94270.00622.42150.0462-0.06420.33050.0159-0.06170.1812-0.1517-0.24980.02040.12760.01190.02710.0740.00530.11879.816528.057363.3036
62.65740.278-1.48373.28941.74534.80270.0402-0.05420.02210.1522-0.05970.27450.024-0.4160.00990.10.0263-0.01080.13780.0170.13884.217425.396362.6548
70.78610.56270.29951.68820.78021.46330.00290.03220.0773-0.0149-0.0064-0.0125-0.08470.04040.00180.0714-0.01280.01040.08470.01250.070931.538431.178544.9923
81.6289-0.61540.292.4905-1.09992.60120.01190.1301-0.214-0.148-0.0311-0.01750.22880.05130.06660.0726-0.00010.00670.1023-0.03330.094935.101715.051638.7819
90.55650.2469-0.16042.15960.22650.9854-0.00150.07020.0773-0.22130.0017-0.153-0.15130.1261-0.00370.0903-0.02210.01040.13070.00680.107940.174533.807742.6574
100.67750.07630.1653.26110.23661.7067-0.0152-0.13370.33110.15950.01720.0293-0.1081-0.0240.0160.1414-0.0490.00190.0882-0.0220.092831.21837.914252.3054
110.93420.1277-0.23551.0806-0.13610.7097-0.0013-0.09690.15560.1438-0.0042-0.0422-0.06270.03850.00790.1516-0.0365-0.00140.1024-0.0160.167238.085947.371161.0227
124.5788-0.34070.78712.01450.34050.7949-0.0150.03750.6725-0.0389-0.0503-0.0012-0.21980.03770.05930.2-0.01820.01950.1295-0.02730.202333.814754.04658.5576
130.7628-0.07620.15380.8774-0.43962.0892-0-0.00440.0503-0.089-0.0105-0.0140.0262-0.01260.01180.08560.0150.00120.072-0.00890.081630.070154.4287101.467
141.79120.5215-0.46081.9496-0.63352.00490.0232-0.21560.07490.1117-0.03180.0848-0.079-0.01810.0140.07470.0105-0.00650.1209-0.02290.069723.693151.2849114.6612
153.3475-0.2885-1.18061.8783-0.61422.39510.0083-0.11230.45250.33820.12430.4426-0.4395-0.56420.02250.18550.06970.01560.19640.00980.159117.432262.7329107.234
161.0181-0.2085-0.27381.3667-0.76011.98760.03080.01190.0988-0.0084-0.0391-0.0608-0.11040.06290.00260.11730.0055-0.0080.0887-0.00330.076229.697159.218293.5255
171.52720.4508-0.41182.55880.05642.1553-0.0510.20250.0376-0.2136-0.01090.1658-0.0021-0.22520.06490.1410.0192-0.01190.13090.01640.105527.762156.973878.757
182.41220.7175-0.46651.9649-1.0841.7490.03320.15390.1804-0.2101-0.03860.12080.043-0.0665-0.01360.20180.0434-0.0160.12670.00150.083428.75959.020178.0353
192.4150.33510.03281.90530.35351.19180.0101-0.0841-0.0925-0.00950.0178-0.11620.03180.06770.00760.0860.0127-0.00270.0858-0.00450.081138.28633.608697.8237
203.52290.4876-0.20642.92450.13313.42150.02980.2631-0.1944-0.19410.08630.32580.1162-0.2087-0.08590.11720.0089-0.05650.1303-0.0050.15513.42931.449594.2955
213.1569-0.8285-1.14562.41440.56342.6343-0.0671-0.0824-0.0479-0.0619-0.03330.04990.02370.00870.07950.0813-0.0197-0.0230.0845-0.0110.092121.156331.2125101.7771
222.29890.5884-1.212.12231.84732.95940.22950.1990.3985-0.2154-0.43580.6904-0.4339-0.3264-0.13030.11670.0538-0.03910.1989-0.03040.274810.393941.3593105.2833
232.3767-0.4354-0.26072.4206-0.26031.5533-0.0415-0.0984-0.18340.0765-0.0570.08950.1171-0.12080.08480.0898-0.00960.0030.1294-0.00750.09817.439827.8346105.6645
243.04-0.6717-0.04991.16770.17621.66850.15780.0877-0.5199-0.0194-0.0326-0.16780.237-0.0618-0.11720.16170.0246-0.00180.12180.00290.166938.41723.493599.2221
252.81260.0881-0.64431.39940.04033.40590.0373-0.1724-0.01740.0337-0.0673-0.0734-0.18980.33830.04180.07130.0088-0.0220.0858-0.02230.094136.394835.943299.36
263.03860.14520.25543.05550.44973.6980.05030.04860.0329-0.05780.0426-0.1942-0.00690.2837-0.05630.11260.01650.04140.1262-0.01290.122252.171734.543696.2577
271.8765-0.47630.0232.49060.36542.43880.0161-0.1101-0.0512-0.13450.0502-0.29370.09030.2813-0.10210.10250.01550.01420.1362-0.00610.170854.192533.481198.1641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 230 through 252 )
2X-RAY DIFFRACTION2chain 'A' and (resid 253 through 331 )
3X-RAY DIFFRACTION3chain 'A' and (resid 332 through 397 )
4X-RAY DIFFRACTION4chain 'A' and (resid 398 through 448 )
5X-RAY DIFFRACTION5chain 'A' and (resid 449 through 500 )
6X-RAY DIFFRACTION6chain 'A' and (resid 501 through 526 )
7X-RAY DIFFRACTION7chain 'B' and (resid 232 through 331 )
8X-RAY DIFFRACTION8chain 'B' and (resid 332 through 377 )
9X-RAY DIFFRACTION9chain 'B' and (resid 378 through 431 )
10X-RAY DIFFRACTION10chain 'B' and (resid 432 through 465 )
11X-RAY DIFFRACTION11chain 'B' and (resid 466 through 508 )
12X-RAY DIFFRACTION12chain 'B' and (resid 509 through 526 )
13X-RAY DIFFRACTION13chain 'C' and (resid 231 through 317 )
14X-RAY DIFFRACTION14chain 'C' and (resid 318 through 387 )
15X-RAY DIFFRACTION15chain 'C' and (resid 388 through 407 )
16X-RAY DIFFRACTION16chain 'C' and (resid 408 through 465 )
17X-RAY DIFFRACTION17chain 'C' and (resid 466 through 500 )
18X-RAY DIFFRACTION18chain 'C' and (resid 501 through 526 )
19X-RAY DIFFRACTION19chain 'D' and (resid 231 through 289 )
20X-RAY DIFFRACTION20chain 'D' and (resid 290 through 319 )
21X-RAY DIFFRACTION21chain 'D' and (resid 320 through 339 )
22X-RAY DIFFRACTION22chain 'D' and (resid 340 through 354 )
23X-RAY DIFFRACTION23chain 'D' and (resid 355 through 397 )
24X-RAY DIFFRACTION24chain 'D' and (resid 398 through 431 )
25X-RAY DIFFRACTION25chain 'D' and (resid 432 through 458 )
26X-RAY DIFFRACTION26chain 'D' and (resid 459 through 500 )
27X-RAY DIFFRACTION27chain 'D' and (resid 501 through 526 )

+
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