[English] 日本語
Yorodumi
- PDB-6o2b: Crystal structure of 4493 Fab in complex with circumsporozoite pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o2b
TitleCrystal structure of 4493 Fab in complex with circumsporozoite protein DND and anti-kappa VHH domain
Components
  • 4493 Fab heavy chain
  • 4493 Kappa light chain
  • Anti-kappa VHH domain
  • Circumsporozoite protein
KeywordsIMMUNE SYSTEM / Malaria / antibody
Function / homology
Function and homology information


entry into host cell by a symbiont-containing vacuole / side of membrane / cell surface / plasma membrane / cytoplasm
Similarity search - Function
: / Plasmodium circumsporozoite protein / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat
Similarity search - Domain/homology
ACETATE ION / Circumsporozoite protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
Plasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsScally, S.W. / Bosch, A. / Prieto, K. / Murugan, R. / Wardemann, H. / Julien, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: Nat. Med. / Year: 2020
Title: Evolution of protective human antibodies against Plasmodium falciparum circumsporozoite protein repeat motifs.
Authors: Murugan, R. / Scally, S.W. / Costa, G. / Mustafa, G. / Thai, E. / Decker, T. / Bosch, A. / Prieto, K. / Levashina, E.A. / Julien, J.P. / Wardemann, H.
History
DepositionFeb 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4493 Fab heavy chain
B: 4493 Kappa light chain
C: 4493 Fab heavy chain
D: 4493 Kappa light chain
H: 4493 Fab heavy chain
I: 4493 Kappa light chain
O: 4493 Fab heavy chain
P: 4493 Kappa light chain
E: Anti-kappa VHH domain
J: Anti-kappa VHH domain
M: Anti-kappa VHH domain
F: Circumsporozoite protein
G: Circumsporozoite protein
K: Circumsporozoite protein
L: Circumsporozoite protein
N: Anti-kappa VHH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,91525
Polymers239,38116
Non-polymers5349
Water23,8701325
1
A: 4493 Fab heavy chain
B: 4493 Kappa light chain
F: Circumsporozoite protein
N: Anti-kappa VHH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0257
Polymers59,8454
Non-polymers1803
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 4493 Fab heavy chain
D: 4493 Kappa light chain
M: Anti-kappa VHH domain
G: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0227
Polymers59,8454
Non-polymers1773
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: 4493 Fab heavy chain
I: 4493 Kappa light chain
E: Anti-kappa VHH domain
K: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9045
Polymers59,8454
Non-polymers591
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
O: 4493 Fab heavy chain
P: 4493 Kappa light chain
J: Anti-kappa VHH domain
L: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9636
Polymers59,8454
Non-polymers1182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.073, 93.405, 94.164
Angle α, β, γ (deg.)82.740, 76.860, 64.450
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 18 or resid 20 through 214))
21(chain C and (resid 1 through 18 or resid 20 through 127 or resid 135 through 214))
31(chain H and (resid 1 through 18 or resid 20 through 127 or resid 135 through 214))
41(chain O and (resid 1 through 18 or resid 20 through 127 or resid 135 through 214))
12(chain B and (resid 1 through 23 or (resid 24...
22chain D
32chain I
42(chain P and (resid 1 through 23 or (resid 24...
13(chain E and resid 2 through 112)
23chain J
33(chain M and resid 2 through 112)
43(chain N and resid 2 through 112)
14chain F
24chain G
34chain K
44chain L

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLULEULEU(chain A and (resid 1 through 18 or resid 20 through 214))AA1 - 181 - 18
121LEULEULYSLYS(chain A and (resid 1 through 18 or resid 20 through 214))AA20 - 21420 - 223
211GLUGLULEULEU(chain C and (resid 1 through 18 or resid 20 through 127 or resid 135 through 214))CC1 - 181 - 18
221LEULEUSERSER(chain C and (resid 1 through 18 or resid 20 through 127 or resid 135 through 214))CC20 - 12720 - 136
231THRTHRLYSLYS(chain C and (resid 1 through 18 or resid 20 through 127 or resid 135 through 214))CC135 - 214144 - 223
311GLUGLULEULEU(chain H and (resid 1 through 18 or resid 20 through 127 or resid 135 through 214))HE1 - 181 - 18
321LEULEUSERSER(chain H and (resid 1 through 18 or resid 20 through 127 or resid 135 through 214))HE20 - 12720 - 136
331THRTHRLYSLYS(chain H and (resid 1 through 18 or resid 20 through 127 or resid 135 through 214))HE135 - 214144 - 223
411GLUGLULEULEU(chain O and (resid 1 through 18 or resid 20 through 127 or resid 135 through 214))OG1 - 181 - 18
421LEULEUSERSER(chain O and (resid 1 through 18 or resid 20 through 127 or resid 135 through 214))OG20 - 12720 - 136
431THRTHRLYSLYS(chain O and (resid 1 through 18 or resid 20 through 127 or resid 135 through 214))OG135 - 214144 - 223
112GLUGLUCYSCYS(chain B and (resid 1 through 23 or (resid 24...BB1 - 231 - 23
122ARGARGALAALA(chain B and (resid 1 through 23 or (resid 24...BB24 - 2524 - 25
132GLUGLUGLUGLU(chain B and (resid 1 through 23 or (resid 24...BB1 - 2131 - 214
142GLUGLUGLUGLU(chain B and (resid 1 through 23 or (resid 24...BB1 - 2131 - 214
152GLUGLUGLUGLU(chain B and (resid 1 through 23 or (resid 24...BB1 - 2131 - 214
162GLUGLUGLUGLU(chain B and (resid 1 through 23 or (resid 24...BB1 - 2131 - 214
212GLUGLUGLUGLUchain DDD1 - 2131 - 214
312GLUGLUGLUGLUchain IIF1 - 2131 - 214
412GLUGLUCYSCYS(chain P and (resid 1 through 23 or (resid 24...PH1 - 231 - 23
422ARGARGALAALA(chain P and (resid 1 through 23 or (resid 24...PH24 - 2524 - 25
432GLUGLUGLUGLU(chain P and (resid 1 through 23 or (resid 24...PH1 - 2131 - 214
442GLUGLUGLUGLU(chain P and (resid 1 through 23 or (resid 24...PH1 - 2131 - 214
452GLUGLUGLUGLU(chain P and (resid 1 through 23 or (resid 24...PH1 - 2131 - 214
462GLUGLUGLUGLU(chain P and (resid 1 through 23 or (resid 24...PH1 - 2131 - 214
113VALVALSERSER(chain E and resid 2 through 112)EI2 - 1122 - 120
213VALVALSERSERchain JJJ2 - 1122 - 120
313VALVALSERSER(chain M and resid 2 through 112)MK2 - 1122 - 120
413VALVALSERSER(chain N and resid 2 through 112)NP2 - 1122 - 120
114ASNASNPROPROchain FFL1 - 121 - 12
214ASNASNPROPROchain GGM1 - 121 - 12
314ASNASNPROPROchain KKN1 - 121 - 12
414ASNASNPROPROchain LLO1 - 121 - 12

NCS ensembles :
ID
1
2
3
4

-
Components

-
Protein/peptide , 1 types, 4 molecules FGKL

#4: Protein/peptide
Circumsporozoite protein / CS


Mass: 1265.286 Da / Num. of mol.: 4 / Fragment: residues 128-139 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893

-
Antibody , 3 types, 12 molecules ACHOBDIPEJMN

#1: Antibody
4493 Fab heavy chain


Mass: 23792.730 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
4493 Kappa light chain


Mass: 23460.979 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody
Anti-kappa VHH domain


Mass: 11326.253 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 3 types, 1334 molecules

#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1325 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20 % (w/v) PEG8000, 0.1 M MES pH 6.0, 0.2 M calcium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 141733 / % possible obs: 97.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 31.7 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.053 / Net I/σ(I): 9.4
Reflection shellResolution: 2.1→2.13 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5870 / CC1/2: 0.641 / Rpim(I) all: 0.349 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In house model

Resolution: 2.1→29.493 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2096 1995 1.41 %
Rwork0.1772 139707 -
obs0.1777 141702 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.12 Å2 / Biso mean: 44.0322 Å2 / Biso min: 18.49 Å2
Refinement stepCycle: final / Resolution: 2.1→29.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16283 0 36 1327 17646
Biso mean--78.31 46.35 -
Num. residues----2257
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3973X-RAY DIFFRACTION8.407TORSIONAL
12C3973X-RAY DIFFRACTION8.407TORSIONAL
13H3973X-RAY DIFFRACTION8.407TORSIONAL
14O3973X-RAY DIFFRACTION8.407TORSIONAL
21B4070X-RAY DIFFRACTION8.407TORSIONAL
22D4070X-RAY DIFFRACTION8.407TORSIONAL
23I4070X-RAY DIFFRACTION8.407TORSIONAL
24P4070X-RAY DIFFRACTION8.407TORSIONAL
31E2235X-RAY DIFFRACTION8.407TORSIONAL
32J2235X-RAY DIFFRACTION8.407TORSIONAL
33M2235X-RAY DIFFRACTION8.407TORSIONAL
34N2235X-RAY DIFFRACTION8.407TORSIONAL
41F216X-RAY DIFFRACTION8.407TORSIONAL
42G216X-RAY DIFFRACTION8.407TORSIONAL
43K216X-RAY DIFFRACTION8.407TORSIONAL
44L216X-RAY DIFFRACTION8.407TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.15250.34881200.2892986497
2.1525-2.21070.2961580.264987397
2.2107-2.27570.29631340.251988697
2.2757-2.34920.24621470.2361996997
2.3492-2.43310.29031460.2275991897
2.4331-2.53040.25871420.2163999697
2.5304-2.64550.22221460.2099992098
2.6455-2.78490.25081380.20011002198
2.7849-2.95920.25551420.19241003498
2.9592-3.18750.20971400.18581000398
3.1875-3.50780.19081450.16921002298
3.5078-4.01430.19231470.15171005998
4.0143-5.05340.15091450.1261006699
5.0534-29.4930.1761450.15291007698
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)
11.63-1.0835-0.56553.24121.27681.7367-0.00040.0532-0.06310.09230.02990.0640.0569-0.0903-0.02780.3405-0.0250.06070.242-0.02330.2796-54.3003-13.65955.454
24.7204-0.21171.49843.3212-0.38762.0339-0.2586-0.3386-0.1540.48380.0548-0.4076-0.11350.08280.18490.37240.1278-0.08270.3453-0.03480.3304-19.2834-24.646955.6378
35.38770.17670.61091.7108-0.56441.5114-0.1769-0.04220.27870.1870.0937-0.1257-0.20910.06190.1130.4486-0.01780.02140.2306-0.04850.3223-41.99995.067756.9995
41.9081-1.9535-1.58085.77582.34183.0146-0.07190.10470.21680.0570.0801-0.58850.150.2469-0.01320.23160.0554-0.05330.3765-0.0010.402-15.669-13.818943.7079
52.3555-0.7098-1.60442.09891.39712.3634-0.06-0.0098-0.1276-0.05540.0924-0.0870.13710.0764-0.02390.2355-0.0260.03080.2353-0.03280.2426-41.7312-58.921210.8671
64.8657-0.41491.99583.04391.09824.14950.1415-0.156-0.41060.4005-0.1283-0.2180.42570.1723-0.00060.3088-0.009-0.03250.28740.07760.3578-6.6371-69.85654.0385
75.84650.4404-0.12030.8994-0.35611.13620.0331-0.30120.6263-0.00760.0336-0.1474-0.20950.2018-0.05060.3477-0.0750.08890.3007-0.12440.431-28.8129-40.809113.502
81.87570.5594-0.21354.39072.64113.99920.02320.0447-0.1729-0.01040.0193-0.20140.18250.0856-0.05180.1966-0.0063-0.02550.32850.01990.321-4.506-57.0889-5.8924
91.0905-0.2031-0.77082.1641.32875.30980.02880.0020.0673-0.1051-0.0121-0.0932-0.0463-0.0666-0.01940.2247-0.01630.03670.2237-0.02340.2595-9.4022.274-8.3656
102.05710.59410.21954.7057-0.23144.2796-0.00860.0325-0.26870.15830.01430.06140.2585-0.1245-0.03780.2567-0.03730.07840.2531-0.04140.2936-25.9593-13.148720.8788
112.66531.9252-1.00545.0139-1.61432.8840.00140.07450.0305-0.47890.00320.34950.4076-0.51540.00240.3969-0.0912-0.05070.4792-0.06760.2969-25.9109-10.3919-16.6545
122.11560.50490.50263.48682.35743.5449-0.11640.04830.0743-0.01380.07450.1884-0.1035-0.26270.04840.32-0.06810.08640.39480.01430.4111-40.9994-9.474415.1348
131.2704-0.3927-0.68352.30111.54963.690.0171-0.02960.09140.05580.0499-0.0685-0.040.0141-0.07320.2143-0.00110.01050.2257-0.02250.265322.6848-38.976738.417
142.30682.2448-0.32826.238-0.90294.22670.0952-0.1447-0.1560.1399-0.0207-0.00660.14010.1274-0.08760.23450.0056-0.01740.3138-0.00850.23234.0836-51.065664.4432
153.2081.462-1.72073.2715-1.18382.5938-0.21270.3009-0.0702-0.30630.19320.08240.377-0.51820.00780.3003-0.0524-0.01730.3726-0.04520.25126.2775-50.661228.2546
161.32360.1616-0.30382.9512.42475.3955-0.0133-0.06450.07720.0370.04580.1096-0.1557-0.4433-0.0170.21910.00980.00490.36450.0330.2194-11.146-47.472259.8006
175.10481.40920.99755.7661.25733.6755-0.12410.3122-0.0373-0.29610.09750.1227-0.2187-0.02060.01270.3211-0.1006-0.00560.4770.04670.3984-55.5531-22.5271-6.3114
183.2161.04780.0874.71110.35111.55020.0382-0.1078-0.2041-0.2469-0.1940.6060.2495-0.80020.11330.4724-0.2243-0.07470.9076-0.03060.4444-26.4386-59.750138.7814
196.16392.35590.18354.24220.59113.59580.03410.12560.49930.0375-0.00540.2503-0.3667-0.0227-0.02170.2846-0.02120.020.32790.01550.36470.4131-29.54331.0064
208.1454-0.44651.57942.00481.8567.8091-0.02011.52750.492-1.14050.1717-0.1668-0.7116-0.2835-0.17620.4963-0.01920.04010.47230.10370.4235-64.83081.067850.3297
218.4651.6468-0.77166.80182.32149.38280.02751.02181.1415-0.65020.28460.1681-0.7413-0.5219-0.29770.30640.0403-0.00060.37590.05520.3952-52.47-43.61429.2893
228.25410.5279-1.74279.17491.19227.3183-0.20830.79461.1745-0.35710.19540.1468-1.4436-0.6726-0.0190.56680.08380.00930.27830.09120.3542-13.22158.2467-25.584
232.26-2.15661.42052.2861-0.27076.3360.15180.41460.6286-0.5153-0.08930.0138-0.4775-0.3029-0.08850.3523-0.02210.03570.25790.01820.366723.6136-36.127619.9658
244.31172.3134-0.82234.85340.11534.02430.0750.1780.3041-0.06370.1583-0.2766-0.42980.3902-0.22210.4054-0.0220.02140.4970.04750.6078-13.119914.508244.5037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 113 )A1 - 113
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 215 )A114 - 215
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 107 )B1 - 107
4X-RAY DIFFRACTION4chain 'B' and (resid 108 through 213 )B108 - 213
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 113 )C1 - 113
6X-RAY DIFFRACTION6chain 'C' and (resid 114 through 214 )C114 - 214
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 107 )D1 - 107
8X-RAY DIFFRACTION8chain 'D' and (resid 108 through 213 )D108 - 213
9X-RAY DIFFRACTION9chain 'H' and (resid 1 through 113 )H1 - 113
10X-RAY DIFFRACTION10chain 'H' and (resid 114 through 214 )H114 - 214
11X-RAY DIFFRACTION11chain 'I' and (resid 1 through 107 )I1 - 107
12X-RAY DIFFRACTION12chain 'I' and (resid 108 through 213 )I108 - 213
13X-RAY DIFFRACTION13chain 'O' and (resid 1 through 113 )O1 - 113
14X-RAY DIFFRACTION14chain 'O' and (resid 114 through 214 )O114 - 214
15X-RAY DIFFRACTION15chain 'P' and (resid 1 through 107 )P1 - 107
16X-RAY DIFFRACTION16chain 'P' and (resid 108 through 213 )P108 - 213
17X-RAY DIFFRACTION17chain 'E' and (resid 2 through 113 )E2 - 113
18X-RAY DIFFRACTION18chain 'J' and (resid 2 through 112 )J2 - 112
19X-RAY DIFFRACTION19chain 'M' and (resid 1 through 113 )M1 - 113
20X-RAY DIFFRACTION20chain 'F' and (resid 1 through 12 )F1 - 12
21X-RAY DIFFRACTION21chain 'G' and (resid 1 through 12 )G1 - 12
22X-RAY DIFFRACTION22chain 'K' and (resid 1 through 12 )K1 - 12
23X-RAY DIFFRACTION23chain 'L' and (resid 1 through 12 )L1 - 12
24X-RAY DIFFRACTION24chain 'N' and (resid 1 through 112 )N1 - 112

+
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