[English] 日本語
Yorodumi
- PDB-5bk3: Crystal structure of the neutralizing anti-circumsporozoite prote... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bk3
TitleCrystal structure of the neutralizing anti-circumsporozoite protein 580 antibody
Components(580 Antibody, ...) x 2
KeywordsIMMUNE SYSTEM / Malaria / Circumsporozoite protein / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsScally, S.W. / Bosch, A. / Triller, G. / Wardemann, H. / Julien, J.P.
CitationJournal: Immunity / Year: 2017
Title: Natural Parasite Exposure Induces Protective Human Anti-Malarial Antibodies.
Authors: Triller, G. / Scally, S.W. / Costa, G. / Pissarev, M. / Kreschel, C. / Bosch, A. / Marois, E. / Sack, B.K. / Murugan, R. / Salman, A.M. / Janse, C.J. / Khan, S.M. / Kappe, S.H.I. / Adegnika, ...Authors: Triller, G. / Scally, S.W. / Costa, G. / Pissarev, M. / Kreschel, C. / Bosch, A. / Marois, E. / Sack, B.K. / Murugan, R. / Salman, A.M. / Janse, C.J. / Khan, S.M. / Kappe, S.H.I. / Adegnika, A.A. / Mordmuller, B. / Levashina, E.A. / Julien, J.P. / Wardemann, H.
History
DepositionSep 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 26, 2020Group: Data collection / Category: chem_comp / reflns / reflns_shell
Item: _chem_comp.type / _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
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 / 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 / _pdbx_struct_assembly_gen.asym_id_list / _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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: 580 Antibody, light chain
H: 580 Antibody, heavy chain
B: 580 Antibody, light chain
A: 580 Antibody, heavy chain
D: 580 Antibody, light chain
C: 580 Antibody, heavy chain
F: 580 Antibody, light chain
E: 580 Antibody, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,21445
Polymers192,5628
Non-polymers5,65237
Water0
1
L: 580 Antibody, light chain
H: 580 Antibody, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,46011
Polymers48,1402
Non-polymers1,3199
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-41 kcal/mol
Surface area19790 Å2
MethodPISA
2
B: 580 Antibody, light chain
A: 580 Antibody, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,74414
Polymers48,1402
Non-polymers1,60312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-73 kcal/mol
Surface area19810 Å2
MethodPISA
3
D: 580 Antibody, light chain
C: 580 Antibody, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,34912
Polymers48,1402
Non-polymers1,20810
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-62 kcal/mol
Surface area19150 Å2
MethodPISA
4
F: 580 Antibody, light chain
E: 580 Antibody, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6628
Polymers48,1402
Non-polymers1,5216
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-14 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.364, 179.567, 140.430
Angle α, β, γ (deg.)90.00, 109.61, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Antibody , 2 types, 8 molecules LBDFHACE

#1: Antibody
580 Antibody, light chain


Mass: 24245.816 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
580 Antibody, heavy chain


Mass: 23894.607 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Sugars , 3 types, 4 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 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]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

-
Non-polymers , 2 types, 33 molecules

#6: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 21
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#7: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.19 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 100 mM MES pH 5, 1.6 M (NH4)2SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 62085 / % possible obs: 99.9 % / Redundancy: 3.9 % / Rpim(I) all: 0.074 / Net I/σ(I): 9.95
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6197 / Rpim(I) all: 0.345 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
SHELXPREPdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I18

5i18


Resolution: 2.8→39.578 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.55
RfactorNum. reflection% reflection
Rfree0.2314 2003 3.23 %
Rwork0.1901 --
obs0.1914 62068 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→39.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13133 0 357 0 13490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813799
X-RAY DIFFRACTIONf_angle_d0.94518795
X-RAY DIFFRACTIONf_dihedral_angle_d15.3148140
X-RAY DIFFRACTIONf_chiral_restr0.0612115
X-RAY DIFFRACTIONf_plane_restr0.0062387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.32821470.29444277X-RAY DIFFRACTION100
2.87-2.94760.31471400.29314279X-RAY DIFFRACTION100
2.9476-3.03430.31031410.28564289X-RAY DIFFRACTION100
3.0343-3.13220.30241450.25654251X-RAY DIFFRACTION100
3.1322-3.24410.26991480.23614275X-RAY DIFFRACTION100
3.2441-3.37390.25491450.22354289X-RAY DIFFRACTION100
3.3739-3.52740.26281360.21594292X-RAY DIFFRACTION100
3.5274-3.71320.29791460.21034300X-RAY DIFFRACTION100
3.7132-3.94570.2541400.1914262X-RAY DIFFRACTION100
3.9457-4.250.1961420.15534280X-RAY DIFFRACTION100
4.25-4.67710.15841390.1274310X-RAY DIFFRACTION100
4.6771-5.35250.17241450.13354292X-RAY DIFFRACTION100
5.3525-6.73810.19781470.17144318X-RAY DIFFRACTION100
6.7381-39.58220.21420.17184351X-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)
12.58551.2956-1.57191.4133-1.34952.87450.06350.1744-0.34840.0165-0.22630.05630.2496-0.02960.15420.47760.0411-0.04430.279-0.1440.389720.060833.566340.0604
26.908-2.9211-2.53415.11311.02542.76270.03990.1383-0.39530.0574-0.1890.610.042-0.53930.11790.3487-0.0989-0.0270.3429-0.0370.4259-6.589440.968465.3742
32.65870.7629-0.77141.73590.5431.3306-0.0271-0.38510.42170.15950.0759-0.4693-0.113-0.04280.05240.4434-0.0131-0.00280.2238-0.03270.202323.049456.625153.458
46.4093-1.5318-0.26072.10210.39432.6240.14330.4234-0.1418-0.1715-0.06420.11080.0087-0.1135-0.0160.322-0.0068-0.00660.1737-0.02630.17528.791753.257544.3497
59.2795-2.53691.26232.8097-0.39252.0377-0.0746-0.03990.3425-0.03330.019-0.0239-0.4282-0.0027-0.04110.3578-0.01150.01830.18630.00440.221331.478859.861447.4315
65.397-1.39-1.50012.09621.08381.52480.18090.395-0.2012-0.2725-0.00190.3318-0.1469-0.0840.02360.30150.01790.00690.2151-0.0270.209119.578456.818145.5777
75.3514-1.5171-0.57492.23530.19041.3706-0.1740.6111-0.5156-0.0057-0.0437-0.02140.50890.03220.09040.3940.01060.010.2424-0.06660.2729.93246.598543.6276
81.80641.2547-1.45111.8502-3.60887.8340.3235-0.14830.09080.41350.00990.3243-0.9327-0.1294-0.03080.36150.0503-0.030.2622-0.09340.34035.355.990164.4574
92.1986-0.21220.57481.306-1.52714.94360.0524-0.0104-0.2208-0.1406-0.06010.17460.142-0.1902-0.03480.3759-0.0073-0.00910.1848-0.07340.29687.063746.510766.5632
102.04370.3411-0.16543.0518-3.6817.09020.1387-0.1346-0.19910.262-0.3281-0.2255-0.47080.35330.28530.3378-0.066-0.02150.2794-0.06490.323411.832549.043973.7406
115.45431.311-0.3990.2927-0.07020.8896-0.0023-0.36920.07910.3955-0.2064-0.4321-1.0190.21890.1980.5423-0.0493-0.0350.3032-0.11440.29848.174152.062676.2022
126.3716-2.53761.51784.3766-0.78335.9144-0.1668-0.74730.75340.66620.051-0.2272-0.24730.39630.17150.404-0.0717-0.01880.4659-0.16180.373653.605544.743529.7521
132.3728-4.133-1.19892.23092.97027.90620.1729-0.62441.24060.5355-0.1997-0.7219-0.96910.43440.01280.5697-0.0839-0.04340.4963-0.11550.708457.302950.567426.5848
147.8477-3.82953.98193.0051-2.65174.6639-0.1681-0.2850.61870.133-0.0487-0.1365-0.2880.12360.21670.43120.0570.04190.3957-0.14770.355946.602545.291324.8003
152.64921.07020.75664.10610.93732.9853-0.0930.3554-0.2724-0.285-0.07030.1841-0.3277-0.81770.17590.44830.12850.01070.6518-0.13060.302521.742338.781712.6865
162.92251.71250.715.93692.15224.05390.06360.3060.0821-0.4191-0.57121.06320.0168-0.84010.51980.43910.124-0.12141.0286-0.17560.465213.031738.250610.9856
175.45430.6465-0.66282.6502-0.08811.04130.0003-0.3235-0.05360.1011-0.07380.09140.00020.1570.0750.40280.11830.01020.43030.07020.238557.380925.587519.7768
182.4094-0.2374-0.45912.3753-0.58391.33310.06130.3343-0.0538-0.188-0.10850.1157-0.0043-0.55840.02980.4234-0.0090.03140.5392-0.13570.274331.012230.2434.5653
193.51571.44631.28894.33751.28322.9925-0.05950.29440.7222-0.3277-0.1428-0.1484-0.98190.18880.19340.7837-0.03330.04150.32920.14810.548846.641195.327642.6615
202.4402-1.20951.12371.3012-0.93833.3249-0.1514-0.10930.6440.7835-0.2737-0.9786-0.83850.95950.37940.8206-0.2272-0.36030.69880.02331.075167.009688.43173.0895
213.1572-3.22651.67584.3647-2.61433.3737-0.0051-0.39780.36330.22040.0219-0.2913-0.0973-0.40810.05440.5601-0.0515-0.0090.28220.02910.311634.839974.771552.5986
226.9249-1.6262-1.24313.799-0.54064.688-0.11970.27530.2133-0.0825-0.1124-0.223-0.4050.35630.10680.4434-0.0884-0.05330.2410.07870.230441.169575.015242.5576
237.8532-7.1432-1.39772.48393.28681.6273-0.08040.25050.02530.1269-0.15050.04040.1958-0.15080.35590.5434-0.034-0.00110.2260.03930.313533.819669.083347.5968
244.3561-4.86913.31878.457-3.89812.2262-0.07750.23620.29960.1002-0.213-0.3919-0.14180.23690.25410.4001-0.08480.00280.2340.04410.266445.779872.105748.6173
251.37530.18890.72270.9361-0.10511.4431-0.42830.1690.59750.1652-0.0442-0.1127-0.8878-0.00170.46430.57970.0162-0.05740.25370.12070.52836.353182.350944.1652
260.89690.27170.13532.24131.89744.03490.03660.025-0.0035-0.020.0791-0.1820.1570.84110.22050.3616-0.0025-0.0080.32450.13720.506954.300266.402162.1774
276.3108-2.0623-0.1665.5411-1.37851.5506-0.3647-0.80450.95090.48990.0813-0.4422-0.4587-0.12750.31570.57390.0189-0.09640.4524-0.02110.39253.463580.779674.3187
282.97120.27422.7426.7555-0.41354.0666-0.0495-1.13851.01470.04640.0474-0.3524-0.995-0.2717-0.00010.4697-0.0458-0.10280.5397-0.13060.481653.510785.718974.5955
299.1631.93841.29147.49344.70352.1362-0.0671-1.23840.41240.8149-0.59881.02340.4353-0.77790.55860.50280.01760.0250.47950.0330.386448.494176.044576.6585
302.0787-0.0042-0.08841.84140.30666.7997-0.1074-0.1976-0.27260.43170.0959-0.0230.54370.24980.06290.53130.1001-0.03070.37070.16080.439324.991274.589523.5881
312.809-1.6635-2.38725.23490.95412.68570.08290.3533-0.5523-0.3637-0.21270.08390.4883-0.06980.12010.49420.0671-0.04050.40960.02350.469220.183873.515315.4303
323.635-0.5165-2.78985.48030.94016.2584-0.09150.5067-0.1096-1.5825-0.0499-0.87381.53210.58580.16230.95460.13240.21460.8114-0.13490.614531.019181.7254-17.247
331.0524-0.56181.29052.17210.81962.64440.02520.8169-0.0376-0.6540.0536-0.7380.2240.66220.02150.63850.16980.17890.7524-0.04550.717533.295482.7059-13.8695
341.3943-1.54620.73712.7944-0.11520.6824-0.5420.2971-0.3727-0.3629-0.3499-0.6978-0.08870.49980.35231.65720.57950.72651.32370.03561.083437.104775.236-21.2581
356.36562.8486-0.40964.1599-1.59083.5872-0.1650.0632-0.3379-0.32980.0616-0.04010.11620.10.05160.49960.18260.04220.38410.07740.29411.846293.549313.3396
363.78361.0318-1.52734.7381-0.88861.08640.0603-0.2298-0.17660.3403-0.11750.1367-0.02910.11060.08130.42560.11030.02130.43270.1120.263112.69994.998117.8866
373.80871.5543-0.54254.487-1.18254.937-0.32971.0747-0.0334-0.74520.48050.52360.4582-0.8182-0.13780.6378-0.0275-0.00330.7910.1240.383419.281488.5575-13.761
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 113 )
2X-RAY DIFFRACTION2chain 'L' and (resid 114 through 211 )
3X-RAY DIFFRACTION3chain 'H' and (resid 1 through 17 )
4X-RAY DIFFRACTION4chain 'H' and (resid 18 through 63 )
5X-RAY DIFFRACTION5chain 'H' and (resid 64 through 82 )
6X-RAY DIFFRACTION6chain 'H' and (resid 82A through 94 )
7X-RAY DIFFRACTION7chain 'H' and (resid 95 through 109 )
8X-RAY DIFFRACTION8chain 'H' and (resid 110 through 134 )
9X-RAY DIFFRACTION9chain 'H' and (resid 135 through 188 )
10X-RAY DIFFRACTION10chain 'H' and (resid 189 through 203 )
11X-RAY DIFFRACTION11chain 'H' and (resid 204 through 214 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 48 )
13X-RAY DIFFRACTION13chain 'B' and (resid 49 through 75 )
14X-RAY DIFFRACTION14chain 'B' and (resid 76 through 113 )
15X-RAY DIFFRACTION15chain 'B' and (resid 114 through 174 )
16X-RAY DIFFRACTION16chain 'B' and (resid 175 through 211 )
17X-RAY DIFFRACTION17chain 'A' and (resid 1 through 109 )
18X-RAY DIFFRACTION18chain 'A' and (resid 110 through 215 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 113 )
20X-RAY DIFFRACTION20chain 'D' and (resid 114 through 211 )
21X-RAY DIFFRACTION21chain 'C' and (resid 1 through 33 )
22X-RAY DIFFRACTION22chain 'C' and (resid 34 through 63 )
23X-RAY DIFFRACTION23chain 'C' and (resid 64 through 82 )
24X-RAY DIFFRACTION24chain 'C' and (resid 82A through 94 )
25X-RAY DIFFRACTION25chain 'C' and (resid 95 through 109 )
26X-RAY DIFFRACTION26chain 'C' and (resid 110 through 119 )
27X-RAY DIFFRACTION27chain 'C' and (resid 120 through 157 )
28X-RAY DIFFRACTION28chain 'C' and (resid 158 through 194 )
29X-RAY DIFFRACTION29chain 'C' and (resid 195 through 213 )
30X-RAY DIFFRACTION30chain 'F' and (resid 1 through 32 )
31X-RAY DIFFRACTION31chain 'F' and (resid 33 through 113 )
32X-RAY DIFFRACTION32chain 'F' and (resid 114 through 150 )
33X-RAY DIFFRACTION33chain 'F' and (resid 151 through 188 )
34X-RAY DIFFRACTION34chain 'F' and (resid 189 through 211 )
35X-RAY DIFFRACTION35chain 'E' and (resid 1 through 51 )
36X-RAY DIFFRACTION36chain 'E' and (resid 52 through 109 )
37X-RAY DIFFRACTION37chain 'E' and (resid 110 through 213 )

+
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