[English] 日本語
Yorodumi
- PDB-6bpc: Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bpc
TitlePlasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to monoclonal antibody 4F7
Components
  • Monoclonal antibody 4F7 Fab heavy chain
  • Monoclonal antibody 4F7 Fab light chain
  • Reticulocyte binding protein 2, putative
KeywordsCELL INVASION / Plasmodium vivax / invasion / malaria / antibody complex
Function / homologyNBD94 domain / Nucleotide-Binding Domain 94 of RH / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Reticulocyte binding protein 2, putative
Function and homology information
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsGruszczyk, J. / Chan, L.J. / Tham, W.H.
CitationJournal: Nature / Year: 2018
Title: Cryo-EM structure of an essential Plasmodium vivax invasion complex.
Authors: Jakub Gruszczyk / Rick K Huang / Li-Jin Chan / Sébastien Menant / Chuan Hong / James M Murphy / Yee-Foong Mok / Michael D W Griffin / Richard D Pearson / Wilson Wong / Alan F Cowman / ...Authors: Jakub Gruszczyk / Rick K Huang / Li-Jin Chan / Sébastien Menant / Chuan Hong / James M Murphy / Yee-Foong Mok / Michael D W Griffin / Richard D Pearson / Wilson Wong / Alan F Cowman / Zhiheng Yu / Wai-Hong Tham /
Abstract: Plasmodium vivax is the most widely distributed malaria parasite that infects humans. P. vivax invades reticulocytes exclusively, and successful entry depends on specific interactions between the P. ...Plasmodium vivax is the most widely distributed malaria parasite that infects humans. P. vivax invades reticulocytes exclusively, and successful entry depends on specific interactions between the P. vivax reticulocyte-binding protein 2b (PvRBP2b) and transferrin receptor 1 (TfR1). TfR1-deficient erythroid cells are refractory to invasion by P. vivax, and anti-PvRBP2b monoclonal antibodies inhibit reticulocyte binding and block P. vivax invasion in field isolates. Here we report a high-resolution cryo-electron microscopy structure of a ternary complex of PvRBP2b bound to human TfR1 and transferrin, at 3.7 Å resolution. Mutational analyses show that PvRBP2b residues involved in complex formation are conserved; this suggests that antigens could be designed that act across P. vivax strains. Functional analyses of TfR1 highlight how P. vivax hijacks TfR1, an essential housekeeping protein, by binding to sites that govern host specificity, without affecting its cellular function of transporting iron. Crystal and solution structures of PvRBP2b in complex with antibody fragments characterize the inhibitory epitopes. Our results establish a structural framework for understanding how P. vivax reticulocyte-binding protein engages its receptor and the molecular mechanism of inhibitory monoclonal antibodies, providing important information for the design of novel vaccine candidates.
History
DepositionNov 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Reticulocyte binding protein 2, putative
B: Monoclonal antibody 4F7 Fab heavy chain
C: Monoclonal antibody 4F7 Fab light chain
D: Reticulocyte binding protein 2, putative
E: Monoclonal antibody 4F7 Fab heavy chain
F: Monoclonal antibody 4F7 Fab light chain


Theoretical massNumber of molelcules
Total (without water)180,5346
Polymers180,5346
Non-polymers00
Water11,169620
1
A: Reticulocyte binding protein 2, putative
B: Monoclonal antibody 4F7 Fab heavy chain
C: Monoclonal antibody 4F7 Fab light chain


Theoretical massNumber of molelcules
Total (without water)90,2673
Polymers90,2673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Reticulocyte binding protein 2, putative
E: Monoclonal antibody 4F7 Fab heavy chain
F: Monoclonal antibody 4F7 Fab light chain


Theoretical massNumber of molelcules
Total (without water)90,2673
Polymers90,2673
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.090, 70.310, 140.363
Angle α, β, γ (deg.)104.180, 100.340, 98.410
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Reticulocyte binding protein 2, putative


Mass: 36519.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (strain Salvador I) (eukaryote)
Strain: Salvador I / Gene: PVX_094255 / Plasmid: pET-32a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: A5K736
#2: Antibody Monoclonal antibody 4F7 Fab heavy chain


Mass: 27428.127 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Monoclonal antibody 4F7 Fab light chain


Mass: 26319.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 620 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M trisodium citrate and 20% (w/v) PEG 3,350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.12
ReflectionResolution: 2.66→66.55 Å / Num. obs: 67863 / % possible obs: 94.3 % / Redundancy: 3.6 % / CC1/2: 0.982 / Net I/σ(I): 6
Reflection shellResolution: 2.66→2.72 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4417 / CC1/2: 0.58 / % possible all: 94.3

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Blu-Icedata collection
iMOSFLM7.2.1data reduction
Aimless0.2.7data scaling
PHENIX1.12_2829phasing
PHENIX1.12_2829model building
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W53,5EN2

5w53

5en2


Resolution: 2.66→66.308 Å / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.42
RfactorNum. reflection% reflection
Rfree0.2148 1009 1.49 %
Rwork0.1973 --
obs0.1996 67840 94.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.2 Å2 / Biso mean: 48.8194 Å2 / Biso min: 14.67 Å2
Refinement stepCycle: final / Resolution: 2.66→66.308 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11425 0 0 620 12045
Biso mean---46.57 -
Num. residues----1430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511686
X-RAY DIFFRACTIONf_angle_d0.67515810
X-RAY DIFFRACTIONf_chiral_restr0.0421735
X-RAY DIFFRACTIONf_plane_restr0.0042008
X-RAY DIFFRACTIONf_dihedral_angle_d4.3427016
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 93 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6626-2.8030.34741240.311995949718
2.803-2.97850.30251420.28894509592
2.9785-3.20840.2611320.245996239755
3.2084-3.5310.22561390.211795159654
3.531-4.04150.21151240.184595519675
4.0415-5.08980.16541270.15194919618
5.0898-37.6860.18821460.176594759621
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)
12.2591.53770.43272.1716-1.18875.1422-0.0202-0.07360.0858-0.23670.20640.42190.5301-0.3552-0.26750.2-0.110.08470.17-0.02670.494969.862941.528211.2638
23.7471.197-1.05014.0907-0.95678.41990.0964-0.5395-0.30910.4282-0.3164-0.6924-0.18380.91630.32190.3266-0.0585-0.0330.32590.00050.582584.978339.854523.7028
31.50371.20890.24811.46010.1060.2887-0.06910.0736-0.033-0.0729-0.1118-0.4435-0.20170.20260.08870.2801-0.49810.14470.0179-0.14690.58981.31647.74225.3218
49.2384-5.9507-7.25444.57585.53348.53450.825-1.33471.9425-0.631-0.2590.0222-0.99730.6588-0.63130.3606-0.08950.11150.3728-0.15380.537780.883647.77224.7853
53.03520.0891-1.80981.35630.21686.09580.29690.78760.1474-0.07380.24670.42890.0176-0.9445-0.44220.2194-0.1050.0390.5798-0.01680.729559.066820.7013-7.372
62.41180.5872-0.47941.59360.16472.694-0.20350.6860.20990.0211-0.0920.2907-0.0974-0.32390.19610.2727-0.17640.01410.37190.00410.553162.506212.7419-2.8886
71.71990.55-0.00593.32610.73233.26260.21740.1928-0.22670.14260.0988-0.15810.2427-0.4561-0.33840.1257-0.0737-0.02190.36420.04770.280269.917417.3411-10.0126
83.7578-0.4453-0.49279.38610.97392.9291-0.274-0.0358-0.10140.11490.4842-0.862-0.01270.3258-0.37060.1428-0.04510.04490.30890.05380.300474.825318.5673-6.8671
93.714-0.51490.97334.1350.81448.1332-0.2898-0.0401-0.7901-0.11320.3168-0.31220.4160.0782-0.09730.2044-0.01170.07520.22720.01690.499173.63049.9125-7.2095
100.5744-0.2904-0.68061.20260.52621.2848-0.06030.1941-0.11410.1001-0.02150.1117-0.0051-0.23110.04160.1888-0.0570.05330.2650.0160.386867.256922.71322.2744
113.08522.57420.13862.5440.79561.25670.23930.00670.18920.175-0.0852-0.0038-0.1379-0.0486-0.16460.3053-0.01440.02320.1135-0.03030.343667.092341.82519.1691
124.6016-5.5874-5.41749.05286.49049.7526-0.29670.7185-0.6743-0.2728-0.4442.4445-0.0089-1.12390.73690.3169-0.0253-0.01890.2403-0.01440.377255.838134.913820.6303
134.4814-1.3507-3.84041.653.70278.5285-0.0760.120.1249-0.3869-0.17591.2523-0.5739-0.5850.16840.49310.057-0.01430.18540.08230.557756.758545.330220.6163
142.5876-2.5968-0.73026.22592.83863.0379-0.06450.1129-0.216-0.50120.2810.12670.08260.1468-0.050.3598-0.08740.08990.16740.06540.312467.026730.55314.5857
152.6415-1.39590.66349.283-0.29714.0370.1369-0.25420.5916-0.2262-0.20920.9518-0.7783-0.0470.07640.4682-0.02810.15910.2584-0.03980.633761.919356.163124.8826
165.21440.73961.22910.68081.96285.71830.2816-0.38080.34460.8281-0.30140.4854-0.1418-0.17560.14690.3834-0.0410.06720.24250.03150.220760.411638.320629.006
171.5582-2.07451.3247.1885-2.70112.2652-0.1014-0.14060.02390.41470.252-0.53840.1829-0.021-0.20510.55310.00290.05270.23410.01310.3707128.183145.971848.5171
182.5383-2.98681.00556.7436-1.51631.1678-0.1127-0.4783-0.53330.07860.54160.54180.2224-0.3607-0.35250.6314-0.06020.06990.24320.04490.4592121.547939.33948.5261
190.39271.104-0.39914.8586-2.87397.7592-0.2446-0.1438-0.5499-0.1170.06050.02680.6459-0.11360.15321.2273-0.1635-0.10730.58160.17631.0664133.52888.550755.9716
202.4939-3.01230.25525.6827-1.56570.79050.4520.2787-0.0192-0.4805-0.2649-0.11580.60640.0182-0.16711.0081-0.0078-0.01980.1606-0.05570.5703130.889827.03443.339
214.2672-2.2660.91582.76542.01794.2183-0.19130.2660.0606-1.22710.3267-0.49550.01250.1942-0.11730.49430.00450.14640.1259-0.06030.3964123.638657.036936.4692
223.93570.54433.53772.00940.95444.8653-0.42460.26360.9186-0.52650.0099-0.8422-0.75170.18330.45030.78090.01280.04780.2336-0.03310.6538128.976273.166741.4595
233.4387-1.0718-0.16834.5561-2.99553.8501-0.1356-0.62940.3661.05920.1302-0.4373-0.4448-0.08340.00520.9490.0505-0.14780.3322-0.08340.5562134.339261.859358.2258
244.4596-1.66860.75572.996-0.68063.0102-0.5009-0.3295-0.46610.77530.5705-0.00920.43230.5991-0.06120.9760.1313-0.08910.4740.0240.5624148.985729.091562.6989
250.9306-2.0520.63337.1363-1.64720.4695-0.22550.06150.2485-0.41210.2049-0.90590.46420.23180.0681.03530.1577-0.01640.2286-0.06890.5957141.988832.13155.2618
262.2455-2.27181.52975.4198-4.31083.5827-0.18640.09630.73810.4829-0.1586-1.1144-0.73520.35960.31880.5768-0.08590.01220.3208-0.03510.7422139.136365.589247.1012
271.5382-2.77791.77466.6937-3.12972.8634-0.2083-0.3390.07560.60240.375-0.28570.0672-0.0589-0.20780.75560.0588-0.0390.2535-0.04140.5371135.128243.688656.4738
283.4426-4.02734.77556.3913-7.66019.1797-0.1105-0.5056-0.4816-1.96610.22360.3135-0.4699-0.8985-0.22961.20790.0802-0.13850.4227-0.04770.7291146.19813.129570.0615
292.776-2.93540.91684.30220.14681.711-0.08470.3863-1.04630.0473-0.24020.71160.4239-0.66330.20610.45-0.17010.08610.3655-0.040.580594.203757.749622.6471
302.5129-0.71791.36972.5114-0.47612.71550.0187-0.3779-0.6149-0.0834-0.09810.36450.5426-0.4248-0.0670.3797-0.16340.08790.1839-0.04970.4097102.537457.159928.6549
313.8749-0.39541.12111.98151.00283.2316-0.2222-0.3221-0.30370.1545-0.04290.1873-0.0317-0.5530.10120.2024-0.05840.10580.1457-0.04590.3826103.417764.50532.0869
328.483-1.7682-0.41045.5195-1.16125.3313-0.2153-0.3023-0.23281.0156-0.10170.75260.1332-0.78940.29850.3882-0.04760.08890.4066-0.07130.203697.728760.432234.7901
335.066-2.412-0.5347.215-3.27119.54610.2148-0.70590.30490.4541-0.53550.2098-0.0716-0.52790.32170.3873-0.09290.08870.4203-0.08160.365988.267169.12628.8548
341.6259-0.7350.67961.25780.39340.9574-0.0362-0.0199-0.25330.11910.10150.24150.2774-0.291-0.00030.3752-0.16620.08120.1118-0.08460.307106.19762.232725.6791
351.6441-0.07991.27611.61170.31712.02760.0581-0.53170.27980.38320.02450.1240.2123-0.3059-0.03410.2776-0.2479-0.01960.21820.0060.39985.754162.35913.0212
361.19341.8405-1.2535.8506-2.62339.3726-0.23330.5675-0.0845-0.69090.1807-0.23940.24740.22180.03090.4457-0.19420.08220.41-0.03760.463491.263260.6668-14.9054
372.74120.3932-1.74410.2466-0.71842.29240.04640.0766-0.0943-0.07540.04040.02430.01980.20260.0890.0022-0.19230.1050.07210.0450.503189.324462.74191.0091
380.96920.9793-0.83481.52820.54276.527-0.209-0.2350.0143-0.15470.1423-0.54170.43171.1362-0.02790.223-0.00050.11110.5019-0.02260.445198.487754.6612-1.565
393.61220.9153-1.25772.9436-0.04444.99030.10630.0634-0.3724-0.1348-0.28430.0050.13940.10180.18390.115-0.1119-0.05720.21210.00230.411191.647959.784-1.1428
404.4121-0.77640.85723.29630.26330.99160.2461-0.1364-0.6146-0.93770.20361.00140.7691-0.5849-0.41420.4849-0.16170.00690.2538-0.04160.670886.975653.8481-9.9715
411.68481.5685-0.81834.1819-1.30746.18220.0463-0.14450.55250.52530.17250.3688-0.9421-0.1111-0.14160.6751-0.00040.02650.0869-0.11830.6495109.166479.87728.9121
421.72030.5186-2.05322.5862-2.40953.771-0.17070.53270.7490.38410.4521-0.35880.0082-0.2433-0.36870.3457-0.1208-0.08990.38110.02240.5103113.733978.50568.6382
431.19460.3494-0.02610.1173-0.26782.6555-0.04080.11070.3760.1752-0.0278-0.0753-0.6007-0.1204-0.04620.497-0.08390.0670.0143-0.05340.4881118.758877.156922.2803
443.66030.0662-0.0691.1297-1.56232.1553-0.11010.4817-0.3691-0.3870.03040.13120.212-0.1271-0.13610.43430.04040.08640.1244-0.03150.3109109.972365.434715.2718
452.10180.56690.16262.12880.0183.8597-0.00920.16750.05990.0242-0.0751-0.161-0.21330.20920.09070.222-0.01130.0080.09170.03350.3694117.461169.985919.7292
465.05940.2355-4.57160.4577-0.81476.0744-0.04840.70640.4425-0.10820.3558-0.0288-0.4321-0.1343-0.35370.1291-0.1795-0.09550.26220.19460.5543112.041176.07513.9155
471.7496-0.18441.53512.7243-0.40663.0335-0.10340.31590.0008-0.62460.25060.4059-0.0378-0.07840.03470.2287-0.08130.0270.2087-0.00780.260889.617167.6634-9.6921
484.34450.58234.31383.40550.22464.4029-0.36320.14720.8087-0.1855-0.0356-0.1998-0.42880.00870.24440.306-0.03350.10270.24390.03140.205596.056677.3667-9.733
496.74811.05414.26444.848-1.51053.7052-0.1225-0.63391.40350.1062-0.0790.9419-0.9485-0.94080.2810.50010.1332-0.05590.3674-0.04650.573283.143680.8519-8.9133
505.58122.52652.24151.54870.30972.24120.2396-0.278-0.14210.1123-0.3411-0.30310.0007-0.20050.08240.2621-0.11320.04420.29580.00180.2712101.889871.6554-1.8538
516.089-1.62813.76443.45370.62618.9455-0.0522-0.28540.2817-0.540.23940.6536-0.1457-0.8739-0.14920.3186-0.0209-0.04240.28490.0820.388978.824472.8443-12.9077
524.5828-0.0170.3261.684-0.62532.2348-0.88661.7920.4301-1.00690.72780.133-0.36940.40220.1380.4445-0.08360.00010.45980.07680.272393.90975.8015-17.5703
535.34411.0906-5.52552.5483-2.23437.7436-0.42260.371-0.21540.2126-0.1634-0.0838-0.2258-0.59760.45580.68750.0224-0.12290.4981-0.08620.6066105.29692.2993-38.8596
547.9725-2.5324-2.6751.95861.64142.09510.5070.4466-0.0809-0.4033-0.32610.0738-0.058-0.2803-0.23890.6357-0.04130.06580.48710.04180.329495.89646.9889-37.5539
557.1209-2.1398-2.12941.97951.31682.1240.69920.93570.0138-0.7872-0.38780.1412-0.1905-0.5667-0.20660.5502-0.0586-0.07870.6280.0710.298280.098413.9052-34.0716
567.3897-0.5392-2.12530.22620.79693.21020.49330.04280.8069-0.21980.2434-0.53670.09070.2686-0.62580.7414-0.11640.10860.5481-0.01620.5244115.85788.3176-44.9345
575.8318-0.4498-1.76395.4084-0.02770.5398-0.3515-0.7142-0.29380.27920.3135-0.63590.16040.6230.10830.669-0.0249-0.10161.4296-0.21980.6451122.8306-0.1149-39.1963
586.8978-1.3021-1.01421.46771.59442.64790.3439-0.56710.03520.0297-0.1076-0.2391-0.04050.4796-0.13160.4822-0.1434-0.09890.43140.1240.357390.76169.7148-27.1361
596.4805-0.722-0.87263.74970.56361.09020.35290.6477-0.8546-0.3923-0.49620.55090.1947-0.85230.03230.8071-0.181-0.25020.7301-0.08630.611874.0999-1.0358-39.7709
604.4308-1.0543-2.29344.27731.84682.68170.27670.0196-0.7879-0.1066-0.59240.21.03910.08160.22781.23070.0462-0.03330.7024-0.01110.4972103.8097-14.1271-51.9566
611.7906-1.56240.75484.1338-2.0561.1115-0.1802-0.5589-0.08030.08810.0298-0.17990.23070.98840.05761.03280.3067-0.0291.02850.05120.4931120.1082-9.9735-50.2155
626.4696-0.7529-3.720.54580.91542.7211-0.3863-0.4023-0.72430.0388-0.0330.14350.39470.16260.32371.0504-0.1003-0.08390.4310.06270.475293.2782-8.1984-41.0683
633.7916-1.0955-3.65210.44691.13463.5474-0.0470.0325-0.5791-0.3034-0.11920.21550.4548-0.22780.31010.9189-0.1012-0.18050.53170.0410.478677.4-1.9022-32.6741
647.3604-2.7871-3.68812.67991.31664.3340.81350.7565-0.12530.1087-0.5359-0.0695-0.06-0.4105-0.24820.86150.0243-0.04690.5908-0.06730.4504107.5713-4.0219-54.1906
651.6544-0.2858-0.95073.51650.57543.8267-0.0646-0.01320.4664-0.29980.0423-0.3823-0.8920.20230.11060.4525-0.1826-0.03060.36380.06320.402878.228133.7077-14.0694
663.8286-1.7913-2.31694.6062.36633.3258-0.28231.15460.2495-1.1125-0.0772-0.3324-0.7075-0.30810.07430.6522-0.17860.06220.52130.12850.380577.994628.9361-27.4022
673.46651.5823-2.52595.85731.08863.2994-0.00450.54030.5034-0.8820.23390.0312-0.8047-0.0373-0.20880.6833-0.09160.0140.52640.09640.27477.730336.3405-22.408
680.140.5021-0.28244.18330.70432.14570.01850.25270.2642-0.0428-0.0856-0.0358-0.56660.05540.12950.3533-0.1164-0.02660.3750.03580.314474.438230.9026-13.9698
690.713-0.07130.010.74880.9251.73420.25940.13460.0974-0.18960.06190.1336-0.2693-0.03-0.21970.3456-0.16810.08670.26410.03060.4473.414147.09255.5256
705.6999-3.89643.8713.3499-2.277.4685-0.062-0.30710.0548-0.19060.05990.02610.40110.2216-0.12090.2636-0.03490.01850.16570.03650.380975.736639.888621.6784
710.13840.2147-0.18080.7249-0.39190.36480.08750.04620.0936-0.0408-0.10670.05720.1673-0.0404-0.08110.0361-0.4040.2018-0.07130.09320.56272.970745.52954.4015
728.14312.63960.59215.0283-2.64033.70320.0297-0.4203-1.096-0.4778-0.627-0.67461.33340.9280.59740.49640.0480.03820.24120.08540.425682.93135.189214.9449
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain E and resid 188:208)E188 - 208
2X-RAY DIFFRACTION2(chain E and resid 209:220)E209 - 220
3X-RAY DIFFRACTION3(chain E and resid 221:232)E221 - 232
4X-RAY DIFFRACTION4(chain E and resid 233:237)E233 - 237
5X-RAY DIFFRACTION5(chain F and resid 25:35)F25 - 35
6X-RAY DIFFRACTION6(chain F and resid 36:52)F36 - 52
7X-RAY DIFFRACTION7(chain F and resid 53:63)F53 - 63
8X-RAY DIFFRACTION8(chain F and resid 64:76)F64 - 76
9X-RAY DIFFRACTION9(chain F and resid 77:93)F77 - 93
10X-RAY DIFFRACTION10(chain F and resid 94:145)F94 - 145
11X-RAY DIFFRACTION11(chain F and resid 146:165)F146 - 165
12X-RAY DIFFRACTION12(chain F and resid 166:170)F166 - 170
13X-RAY DIFFRACTION13(chain F and resid 171:186)F171 - 186
14X-RAY DIFFRACTION14(chain F and resid 187:202)F187 - 202
15X-RAY DIFFRACTION15(chain F and resid 203:215)F203 - 215
16X-RAY DIFFRACTION16(chain F and resid 216:235)F216 - 235
17X-RAY DIFFRACTION17(chain A and resid 171:212)A171 - 212
18X-RAY DIFFRACTION18(chain A and resid 213:258)A213 - 258
19X-RAY DIFFRACTION19(chain A and resid 259:265)A259 - 265
20X-RAY DIFFRACTION20(chain A and resid 266:294)A266 - 294
21X-RAY DIFFRACTION21(chain A and resid 295:308)A295 - 308
22X-RAY DIFFRACTION22(chain A and resid 309:321)A309 - 321
23X-RAY DIFFRACTION23(chain A and resid 322:335)A322 - 335
24X-RAY DIFFRACTION24(chain A and resid 336:369)A336 - 369
25X-RAY DIFFRACTION25(chain A and resid 370:395)A370 - 395
26X-RAY DIFFRACTION26(chain A and resid 396:420)A396 - 420
27X-RAY DIFFRACTION27(chain A and resid 421:457)A421 - 457
28X-RAY DIFFRACTION28(chain A and resid 458:466)A458 - 466
29X-RAY DIFFRACTION29(chain B and resid 20:35)B20 - 35
30X-RAY DIFFRACTION30(chain B and resid 36:59)B36 - 59
31X-RAY DIFFRACTION31(chain B and resid 60:77)B60 - 77
32X-RAY DIFFRACTION32(chain B and resid 78:101)B78 - 101
33X-RAY DIFFRACTION33(chain B and resid 102:108)B102 - 108
34X-RAY DIFFRACTION34(chain B and resid 109:128)B109 - 128
35X-RAY DIFFRACTION35(chain B and resid 129:146)B129 - 146
36X-RAY DIFFRACTION36(chain B and resid 147:158)B147 - 158
37X-RAY DIFFRACTION37(chain B and resid 159:174)B159 - 174
38X-RAY DIFFRACTION38(chain B and resid 175:186)B175 - 186
39X-RAY DIFFRACTION39(chain B and resid 187:230)B187 - 230
40X-RAY DIFFRACTION40(chain B and resid 231:237)B231 - 237
41X-RAY DIFFRACTION41(chain C and resid 24:29)C24 - 29
42X-RAY DIFFRACTION42(chain C and resid 30:40)C30 - 40
43X-RAY DIFFRACTION43(chain C and resid 41:58)C41 - 58
44X-RAY DIFFRACTION44(chain C and resid 59:69)C59 - 69
45X-RAY DIFFRACTION45(chain C and resid 70:125)C70 - 125
46X-RAY DIFFRACTION46(chain C and resid 126:130)C126 - 130
47X-RAY DIFFRACTION47(chain C and resid 131:158)C131 - 158
48X-RAY DIFFRACTION48(chain C and resid 159:174)C159 - 174
49X-RAY DIFFRACTION49(chain C and resid 175:183)C175 - 183
50X-RAY DIFFRACTION50(chain C and resid 184:200)C184 - 200
51X-RAY DIFFRACTION51(chain C and resid 201:218)C201 - 218
52X-RAY DIFFRACTION52(chain C and resid 219:235)C219 - 235
53X-RAY DIFFRACTION53(chain D and resid 171:186)D171 - 186
54X-RAY DIFFRACTION54(chain D and resid 187:200)D187 - 200
55X-RAY DIFFRACTION55(chain D and resid 201:229)D201 - 229
56X-RAY DIFFRACTION56(chain D and resid 230:264)D230 - 264
57X-RAY DIFFRACTION57(chain D and resid 265:279)D265 - 279
58X-RAY DIFFRACTION58(chain D and resid 280:313)D280 - 313
59X-RAY DIFFRACTION59(chain D and resid 314:335)D314 - 335
60X-RAY DIFFRACTION60(chain D and resid 336:359)D336 - 359
61X-RAY DIFFRACTION61(chain D and resid 360:381)D360 - 381
62X-RAY DIFFRACTION62(chain D and resid 382:405)D382 - 405
63X-RAY DIFFRACTION63(chain D and resid 406:435)D406 - 435
64X-RAY DIFFRACTION64(chain D and resid 436:461)D436 - 461
65X-RAY DIFFRACTION65(chain E and resid 20:68)E20 - 68
66X-RAY DIFFRACTION66(chain E and resid 69:79)E69 - 79
67X-RAY DIFFRACTION67(chain E and resid 80:102)E80 - 102
68X-RAY DIFFRACTION68(chain E and resid 103:129)E103 - 129
69X-RAY DIFFRACTION69(chain E and resid 130:158)E130 - 158
70X-RAY DIFFRACTION70(chain E and resid 159:165)E159 - 165
71X-RAY DIFFRACTION71(chain E and resid 166:176)E166 - 176
72X-RAY DIFFRACTION72(chain E and resid 177:187)E177 - 187

+
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