[English] 日本語
Yorodumi
- PDB-6o2a: Crystal structure of 4493 Fab in complex with circumsporozoite pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o2a
TitleCrystal structure of 4493 Fab in complex with circumsporozoite protein NDN 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
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: 2.15 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

-
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
F: Circumsporozoite protein
G: Circumsporozoite protein
K: Circumsporozoite protein
L: Circumsporozoite protein
M: Anti-kappa VHH domain
N: Anti-kappa VHH domain
J: Anti-kappa VHH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,38234
Polymers239,26516
Non-polymers1,11718
Water12,268681
1
A: 4493 Fab heavy chain
B: 4493 Kappa light chain
E: Anti-kappa VHH domain
F: Circumsporozoite protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,18910
Polymers59,8164
Non-polymers3726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 4493 Fab heavy chain
D: 4493 Kappa light chain
G: Circumsporozoite protein
M: Anti-kappa VHH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,18910
Polymers59,8164
Non-polymers3726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: 4493 Fab heavy chain
I: 4493 Kappa light chain
K: Circumsporozoite protein
N: Anti-kappa VHH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0027
Polymers59,8164
Non-polymers1863
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
O: 4493 Fab heavy chain
P: 4493 Kappa light chain
L: Circumsporozoite protein
J: Anti-kappa VHH domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0027
Polymers59,8164
Non-polymers1863
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.654, 90.728, 92.515
Angle α, β, γ (deg.)89.380, 64.290, 76.880
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...
21(chain C and (resid 1 through 12 or (resid 13...
31(chain H and (resid 1 through 12 or (resid 13...
41(chain O and (resid 1 through 12 or (resid 13...
12(chain B and (resid 1 through 23 or (resid 24...
22(chain D and (resid 1 through 23 or (resid 24...
32(chain I and (resid 1 through 53 or (resid 54...
42(chain P and resid 1 through 213)
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...AA1 - 181 - 18
121LEULEUVALVAL(chain A and (resid 1 through 18 or resid 20...AA20 - 6320 - 66
131LYSLYSLYSLYS(chain A and (resid 1 through 18 or resid 20...AA6467
141GLUGLUCYSCYS(chain A and (resid 1 through 18 or resid 20...AA1 - 2161 - 225
151GLUGLUCYSCYS(chain A and (resid 1 through 18 or resid 20...AA1 - 2161 - 225
161GLUGLUCYSCYS(chain A and (resid 1 through 18 or resid 20...AA1 - 2161 - 225
171GLUGLUCYSCYS(chain A and (resid 1 through 18 or resid 20...AA1 - 2161 - 225
211GLUGLUVALVAL(chain C and (resid 1 through 12 or (resid 13...CC1 - 121 - 12
221GLNGLNGLNGLN(chain C and (resid 1 through 12 or (resid 13...CC1313
231GLUGLULYSLYS(chain C and (resid 1 through 12 or (resid 13...CC1 - 2141 - 223
241GLUGLULYSLYS(chain C and (resid 1 through 12 or (resid 13...CC1 - 2141 - 223
251GLUGLULYSLYS(chain C and (resid 1 through 12 or (resid 13...CC1 - 2141 - 223
261GLUGLULYSLYS(chain C and (resid 1 through 12 or (resid 13...CC1 - 2141 - 223
311GLUGLUVALVAL(chain H and (resid 1 through 12 or (resid 13...HE1 - 121 - 12
321GLNGLNGLNGLN(chain H and (resid 1 through 12 or (resid 13...HE1313
331GLUGLUSERSER(chain H and (resid 1 through 12 or (resid 13...HE1 - 2151 - 224
341GLUGLUSERSER(chain H and (resid 1 through 12 or (resid 13...HE1 - 2151 - 224
351GLUGLUSERSER(chain H and (resid 1 through 12 or (resid 13...HE1 - 2151 - 224
361GLUGLUSERSER(chain H and (resid 1 through 12 or (resid 13...HE1 - 2151 - 224
411GLUGLUVALVAL(chain O and (resid 1 through 12 or (resid 13...OG1 - 121 - 12
421GLNGLNGLNGLN(chain O and (resid 1 through 12 or (resid 13...OG1313
431GLUGLUSERSER(chain O and (resid 1 through 12 or (resid 13...OG1 - 2151 - 224
441GLUGLUSERSER(chain O and (resid 1 through 12 or (resid 13...OG1 - 2151 - 224
451GLUGLUSERSER(chain O and (resid 1 through 12 or (resid 13...OG1 - 2151 - 224
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
132GLUGLUCYSCYS(chain B and (resid 1 through 23 or (resid 24...BB1 - 2141 - 215
142GLUGLUCYSCYS(chain B and (resid 1 through 23 or (resid 24...BB1 - 2141 - 215
152GLUGLUCYSCYS(chain B and (resid 1 through 23 or (resid 24...BB1 - 2141 - 215
162GLUGLUCYSCYS(chain B and (resid 1 through 23 or (resid 24...BB1 - 2141 - 215
212GLUGLUCYSCYS(chain D and (resid 1 through 23 or (resid 24...DD1 - 231 - 23
222ARGARGALAALA(chain D and (resid 1 through 23 or (resid 24...DD24 - 2524 - 25
232GLUGLUGLUGLU(chain D and (resid 1 through 23 or (resid 24...DD1 - 2131 - 214
242GLUGLUGLUGLU(chain D and (resid 1 through 23 or (resid 24...DD1 - 2131 - 214
252GLUGLUGLUGLU(chain D and (resid 1 through 23 or (resid 24...DD1 - 2131 - 214
262GLUGLUGLUGLU(chain D and (resid 1 through 23 or (resid 24...DD1 - 2131 - 214
312GLUGLUSERSER(chain I and (resid 1 through 53 or (resid 54...IF1 - 531 - 54
322ARGARGALAALA(chain I and (resid 1 through 53 or (resid 54...IF54 - 5555 - 56
332GLUGLUGLUGLU(chain I and (resid 1 through 53 or (resid 54...IF1 - 2131 - 214
342GLUGLUGLUGLU(chain I and (resid 1 through 53 or (resid 54...IF1 - 2131 - 214
352GLUGLUGLUGLU(chain I and (resid 1 through 53 or (resid 54...IF1 - 2131 - 214
362GLUGLUGLUGLU(chain I and (resid 1 through 53 or (resid 54...IF1 - 2131 - 214
412GLUGLUGLUGLU(chain P and resid 1 through 213)PH1 - 2131 - 214
113VALVALSERSER(chain E and resid 2 through 112)EI2 - 1122 - 120
213VALVALSERSERchain JJP2 - 1122 - 120
313VALVALSERSER(chain M and resid 2 through 112)MN2 - 1122 - 120
413VALVALSERSER(chain N and resid 2 through 112)NO2 - 1122 - 120
114ASNASNASNASNchain FFJ1 - 91 - 9
214ASNASNASNASNchain GGK1 - 91 - 9
314ASNASNASNASNchain KKL1 - 91 - 9
414ASNASNASNASNchain LLM1 - 91 - 9

NCS ensembles :
ID
1
2
3
4

-
Components

-
Protein/peptide , 1 types, 4 molecules FGKL

#4: Protein/peptide
Circumsporozoite protein / / CS


Mass: 1236.248 Da / Num. of mol.: 4 / Fragment: residues 124-135 / Source method: obtained synthetically
Source: (synth.) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: P02893

-
Antibody , 3 types, 12 molecules ACHOBDIPEMNJ

#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 , 2 types, 699 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 681 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20 % (w/v) PEG3350, 0.2 M potassium nitrate

-
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: 2.15→30 Å / Num. obs: 124730 / % possible obs: 97.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 39.7 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.044 / Net I/σ(I): 10.5
Reflection shellResolution: 2.15→2.18 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5069 / CC1/2: 0.722 / Rpim(I) all: 0.339 / % possible all: 96.9

-
Processing

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

Resolution: 2.15→29.415 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2211 1357 1.09 %
Rwork0.1928 123305 -
obs0.1932 124662 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.93 Å2 / Biso mean: 54.1797 Å2 / Biso min: 24.25 Å2
Refinement stepCycle: final / Resolution: 2.15→29.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16260 0 72 681 17013
Biso mean--65.46 51.67 -
Num. residues----2259
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3989X-RAY DIFFRACTION8.971TORSIONAL
12C3989X-RAY DIFFRACTION8.971TORSIONAL
13H3989X-RAY DIFFRACTION8.971TORSIONAL
14O3989X-RAY DIFFRACTION8.971TORSIONAL
21B4077X-RAY DIFFRACTION8.971TORSIONAL
22D4077X-RAY DIFFRACTION8.971TORSIONAL
23I4077X-RAY DIFFRACTION8.971TORSIONAL
24P4077X-RAY DIFFRACTION8.971TORSIONAL
31E2247X-RAY DIFFRACTION8.971TORSIONAL
32J2247X-RAY DIFFRACTION8.971TORSIONAL
33M2247X-RAY DIFFRACTION8.971TORSIONAL
34N2247X-RAY DIFFRACTION8.971TORSIONAL
41F162X-RAY DIFFRACTION8.971TORSIONAL
42G162X-RAY DIFFRACTION8.971TORSIONAL
43K162X-RAY DIFFRACTION8.971TORSIONAL
44L162X-RAY DIFFRACTION8.971TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.15-2.22680.31451360.31121223197
2.2268-2.31590.34671330.2951220197
2.3159-2.42130.32641350.28391230097
2.4213-2.54890.3051360.25791227797
2.5489-2.70850.28421350.2331232498
2.7085-2.91740.24911370.22281241598
2.9174-3.21070.25711350.21211233998
3.2107-3.67450.20251370.18611238298
3.6745-4.62660.17511360.14911243198
4.6266-29.4150.17091370.15131240598
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)
12.0323-0.42380.1542.5283-1.23182.5138-0.1068-0.05090.01620.11940.0790.1884-0.0421-0.21250.03420.30710.09360.0240.43130.00820.2504-51.793351.787811.3828
22.65470.8926-0.69572.193-0.29333.4955-0.1392-0.33640.14970.06620.0983-0.1287-0.40450.21020.04470.42990.0217-0.08770.35780.01410.2611-15.822450.728423.802
33.96820.5711-0.55851.6672-0.13520.4402-0.07190.39980.0893-0.28450.03510.1167-0.0538-0.11570.06130.40120.061-0.03210.45750.04660.2338-38.59154.443-6.3299
41.318-0.5728-0.11912.7835-1.66792.7125-0.0816-0.1512-0.17150.23490.0298-0.108-0.09830.14010.05050.2912-0.0417-0.04030.34580.01670.2652-12.792740.046712.71
53.4306-0.1441-0.35621.6464-1.19342.3690.26840.30310.25530.1404-0.18150.2042-0.3014-0.1668-0.07670.47280.12050.13360.38130.03630.3556-39.65584.439254.1878
63.11030.56950.17241.9577-0.46030.99740.0925-0.3170.3501-0.07720.3408-0.4279-0.89871.0911-0.31210.5545-0.27220.04890.7421-0.15950.4298-5.3131.807464.1359
74.9541.073-1.18771.60680.37732.90730.01570.63280.1639-0.2050.05770.054-0.4034-0.2089-0.04410.58170.15560.07710.5520.10020.318-27.50137.156535.3829
81.9281-0.6973-0.87882.5423-1.60813.3799-0.1037-0.19620.02720.1310.1871-0.2792-0.23560.4492-0.03240.3511-0.0503-0.03860.5495-0.12190.4104-1.8932-9.147552.6206
91.29890.1129-0.43594.8117-1.6383.08590.170.0259-0.09730.0372-0.19290.0194-0.04780.3841-0.00070.20190.00480.00460.3539-0.00010.2685-5.2628-7.8196-6.9617
102.6894-0.18980.2853.3428-0.16384.1411-0.0209-0.18520.03740.0626-0.08160.0076-0.08450.09420.10320.3291-0.03770.07980.2362-0.01620.313-23.675918.36749.6605
113.0993-0.6531-1.33821.7334-0.38013.74820.008-0.0116-0.11540.3285-0.02510.50830.3589-0.13150.02420.402-0.08350.050.2606-0.01710.5402-22.6964-17.96032.7572
122.14460.3666-0.04614.4644-1.53371.6174-0.15880.1826-0.1451-0.2586-0.0580.23190.1329-0.09620.22330.4136-0.0520.08410.3686-0.09750.3752-38.349913.39854.5048
134.4601-0.3618-1.76423.0389-0.48642.271-0.02870.4644-0.8516-0.033-0.1010.11210.0128-0.05580.12540.25640.00090.00520.3009-0.03660.418424.506932.874135.2808
143.5862-0.88330.50834.3241-0.20392.99290.067-0.22830.2978-0.0409-0.012-0.2736-0.05640.0894-0.03390.34170.00660.03290.22870.03580.24726.752457.863150.5222
152.6493-0.6921-0.85740.58630.28970.5956-0.7765-0.0149-2.93460.348-0.12840.46351.2147-0.6283-0.56230.4404-0.33480.2861-0.06450.05881.37068.701422.182347.0847
162.19640.3147-0.30674.2148-1.90492.29270.105-0.00580.1603-0.1087-0.19840.2288-0.2186-0.14650.12520.4090.004-0.02840.3201-0.03210.255-8.65653.49747.124
173.5348-1.7188-1.48373.2581-0.23053.64730.29530.4162-0.0973-0.2642-0.4625-0.39450.03290.14890.18540.25780.0064-0.01510.39610.02710.3272-8.596543.5777-15.5287
182.00850.3665-1.33816.161-0.09157.3707-0.0302-0.3888-0.0621-0.1535-0.4310.73451.0454-1.05480.44180.5524-0.10030.01050.8647-0.00760.5274-63.551249.29-1.6053
198.3792-1.0779-4.29866.60561.57727.0288-0.03710.55870.4811-0.0586-0.35590.42080.1471-1.44270.43090.53970.2487-0.01971.06190.0540.5693-52.38444.309141.4607
203.5322-0.6686-3.47467.56670.55673.5161-1.25690.5067-0.2874-0.380.4171-0.44791.16760.58850.80870.55240.0430.12470.6718-0.11490.6103-4.2311-23.9219-14.2221
210.30090.56660.3261.54580.32150.5232-0.11270.2175-0.2486-0.43410.27280.0583-0.05890.1470.08090.5379-0.20660.13450.4332-0.42651.4927.86615.748431.1643
225.347-0.3573-2.95593.2155-0.83134.75210.05260.8624-0.2085-0.6414-0.1878-0.19230.1166-0.45160.13070.5016-0.01570.090.7561-0.10470.52921.4046-5.292124.3871
235.16440.4493-1.22772.6954-0.77314.1919-0.0453-0.1631-0.5005-0.03010.05490.44430.2769-0.4429-0.02590.4994-0.06750.11110.488-0.0410.7341-53.8633-8.900414.479
246.1210.7901-1.21673.749-0.91265.1838-0.07970.0021-0.16530.0604-0.10310.2649-0.1057-0.5160.16650.3151-0.01530.00410.3977-0.040.3712-23.623131.26657.8292
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 216 )A114 - 216
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 107 )B1 - 107
4X-RAY DIFFRACTION4chain 'B' and (resid 108 through 214 )B108 - 214
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 215 )H114 - 215
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 215 )O114 - 215
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 1 through 113 )E1 - 113
18X-RAY DIFFRACTION18chain 'F' and (resid 1 through 9 )F1 - 9
19X-RAY DIFFRACTION19chain 'G' and (resid 1 through 9 )G1 - 9
20X-RAY DIFFRACTION20chain 'K' and (resid 1 through 9 )K1 - 9
21X-RAY DIFFRACTION21chain 'L' and (resid 1 through 9 )L1 - 9
22X-RAY DIFFRACTION22chain 'M' and (resid 1 through 112 )M1 - 112
23X-RAY DIFFRACTION23chain 'N' and (resid 2 through 112 )N2 - 112
24X-RAY DIFFRACTION24chain 'J' and (resid 2 through 112 )J2 - 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