[English] 日本語
Yorodumi
- PDB-8u70: Crystal structure of malaria transmission-blocking anti-Pfs48/45 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8u70
TitleCrystal structure of malaria transmission-blocking anti-Pfs48/45 antibody RUPA-58.
Components
  • Antibody RUPA-58 Heavy chain
  • Antibody RUPA-58 Kappa chain
KeywordsIMMUNE SYSTEM / Pfs48/45 / human transmission-blocking antibodies / Malaria
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsHailemariam, S. / Ivanochko, D. / Julien, J.P.
Funding support Canada, United States, 5items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)428410 Canada
CIFAR Azrieli Global Scholars Canada
Ontario Early Researcher Awards Canada
Canada Research Chairs Canada
Bill & Melinda Gates FoundationOPP1170236 United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural elucidation of full-length Pfs48/45 in complex with potent monoclonal antibodies isolated from a naturally exposed individual.
Authors: Iga Kucharska / Danton Ivanochko / Sophia Hailemariam / Maartje R Inklaar / Hee Ryung Kim / Karina Teelen / Rianne Stoter / Marga van de Vegte-Bolmer / Geert-Jan van Gemert / Anthony Semesi ...Authors: Iga Kucharska / Danton Ivanochko / Sophia Hailemariam / Maartje R Inklaar / Hee Ryung Kim / Karina Teelen / Rianne Stoter / Marga van de Vegte-Bolmer / Geert-Jan van Gemert / Anthony Semesi / Brandon McLeod / Ahyoung Ki / Won-Kyu Lee / John L Rubinstein / Matthijs M Jore / Jean-Philippe Julien /
Abstract: Biomedical interventions that block the transmission of Plasmodium falciparum (Pf) from humans to mosquitoes may be critical for malaria elimination. Pfs48/45, a gamete-surface protein essential for ...Biomedical interventions that block the transmission of Plasmodium falciparum (Pf) from humans to mosquitoes may be critical for malaria elimination. Pfs48/45, a gamete-surface protein essential for Pf development in the mosquito midgut, is a target of clinical-stage transmission-blocking vaccines and monoclonal antibodies (mAbs) that disrupt Pf transmission to mosquitoes. Antibodies directed to domain 3 of Pfs48/45 have been structurally and functionally described; however, in-depth information about other inhibitory epitopes on Pfs48/45 is currently limited. Here, we present a cryo-electron microscopy structure of full-length Pfs48/45 in complex with potent human mAbs targeting all three domains. Our data indicate that although Pfs48/45 domains 1 and 2 are rigidly coupled, there is substantial conformational flexibility between domains 2 and 3. Characterization of mAbs against domain 1 revealed the presence of a conformational epitope class that is largely conserved across Pf field isolates and is associated with recognition by potent antibodies. Our study provides insights into epitopes across full-length Pfs48/45 and has implications for the design of next-generation malaria interventions.
History
DepositionSep 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antibody RUPA-58 Kappa chain
C: Antibody RUPA-58 Kappa chain
E: Antibody RUPA-58 Kappa chain
I: Antibody RUPA-58 Kappa chain
K: Antibody RUPA-58 Kappa chain
B: Antibody RUPA-58 Heavy chain
D: Antibody RUPA-58 Heavy chain
F: Antibody RUPA-58 Heavy chain
J: Antibody RUPA-58 Heavy chain
L: Antibody RUPA-58 Heavy chain
G: Antibody RUPA-58 Kappa chain
H: Antibody RUPA-58 Heavy chain


Theoretical massNumber of molelcules
Total (without water)287,31912
Polymers287,31912
Non-polymers00
Water00
1
A: Antibody RUPA-58 Kappa chain
B: Antibody RUPA-58 Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,8862
Polymers47,8862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-23 kcal/mol
Surface area19530 Å2
MethodPISA
2
C: Antibody RUPA-58 Kappa chain
D: Antibody RUPA-58 Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,8862
Polymers47,8862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-21 kcal/mol
Surface area19720 Å2
MethodPISA
3
E: Antibody RUPA-58 Kappa chain
F: Antibody RUPA-58 Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,8862
Polymers47,8862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-23 kcal/mol
Surface area20020 Å2
MethodPISA
4
I: Antibody RUPA-58 Kappa chain
J: Antibody RUPA-58 Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,8862
Polymers47,8862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-21 kcal/mol
Surface area19840 Å2
MethodPISA
5
K: Antibody RUPA-58 Kappa chain
L: Antibody RUPA-58 Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,8862
Polymers47,8862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-22 kcal/mol
Surface area19380 Å2
MethodPISA
6
G: Antibody RUPA-58 Kappa chain
H: Antibody RUPA-58 Heavy chain


Theoretical massNumber of molelcules
Total (without water)47,8862
Polymers47,8862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-20 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.513, 164.513, 92.276
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Antibody
Antibody RUPA-58 Kappa chain


Mass: 23470.133 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): epithelial / Cell line (production host): 293F / Production host: Homo sapiens (human) / Tissue (production host): embryonic kidney
#2: Antibody
Antibody RUPA-58 Heavy chain


Mass: 24416.352 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): epithelial / Cell line (production host): 239F / Production host: Homo sapiens (human) / Tissue (production host): embryonic kidney
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium acetate, 30% PEG 8000, 0.1 M sodium cacodylate, 20% ethylene glycol

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.09→29.46 Å / Num. obs: 51007 / % possible obs: 99.7 % / Redundancy: 9.5 % / Biso Wilson estimate: 51.7 Å2 / CC1/2: 0.957 / Rpim(I) all: 0.152 / Net I/σ(I): 3.6
Reflection shellResolution: 3.09→3.2 Å / Redundancy: 9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5024 / CC1/2: 0.336 / Rpim(I) all: 0.517 / % possible all: 99

-
Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX(1.20.1_4487)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.09→29.46 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2631 1798 3.53 %
Rwork0.2231 --
obs0.2245 51007 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.09→29.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19914 0 0 0 19914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00420388
X-RAY DIFFRACTIONf_angle_d0.90727720
X-RAY DIFFRACTIONf_dihedral_angle_d14.357356
X-RAY DIFFRACTIONf_chiral_restr0.0563096
X-RAY DIFFRACTIONf_plane_restr0.0073552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.170.3531360.3173739X-RAY DIFFRACTION100
3.17-3.270.37741360.31293755X-RAY DIFFRACTION100
3.27-3.370.38711340.30693850X-RAY DIFFRACTION100
3.37-3.490.3611480.28163762X-RAY DIFFRACTION100
3.49-3.630.30731380.24983820X-RAY DIFFRACTION100
3.63-3.80.27141330.23153778X-RAY DIFFRACTION100
3.8-40.24811460.22853780X-RAY DIFFRACTION100
4-4.250.2551360.20023763X-RAY DIFFRACTION100
4.25-4.570.23921350.18293824X-RAY DIFFRACTION100
4.57-5.030.2351380.1883783X-RAY DIFFRACTION100
5.03-5.750.23781500.19423807X-RAY DIFFRACTION100
5.76-7.230.24451390.23083784X-RAY DIFFRACTION100
7.23-29.460.19741290.19293764X-RAY DIFFRACTION99
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)
15.82393.740.79892.11382.19874.47540.3480.16680.20770.1215-0.55790.1771-0.1949-0.06620.15540.47480.0368-0.03770.42470.01970.281613.69324.6559-8.3264
24.58771.7983-1.56514.205-1.63291.8717-0.43130.51960.0458-0.82720.08120.0570.0213-0.20830.10540.503-0.0404-0.08460.41820.00940.29854.866220.281-7.5144
33.23741.1290.17820.77510.19820.1858-0.0214-0.03440.0354-0.0673-0.0775-0.00510.13220.13310.08060.44310.0852-0.00020.39370.03620.295619.517527.98811.9196
46.2676-1.88142.77682.442-0.94392.97460.0950.0322-0.50680.3866-0.1578-0.13410.23210.4993-0.14220.4555-0.01320.00760.60270.09120.58938.133326.32979.3455
56.0713-1.80282.76821.7892-0.89161.98770.24660.37140.63310.2087-0.4914-0.42140.30150.55390.28340.3863-0.0520.09860.74630.13760.43948.114930.99516.995
62.86820.1252.7899.26591.28663.43940.1063-0.401-0.40940.8693-0.2142-0.18510.1282-0.0269-0.01090.50780.0131-0.0340.3650.02520.3926-20.459775.684114.9914
71.1118-0.91120.66435.70691.15583.0681-0.056-0.1598-0.08170.514-0.26120.44030.1039-0.02420.24970.3464-0.09920.02510.46520.04820.3803-23.498384.834711.7109
82.28941.898-0.9437.62651.5482.40370.1321-0.0510.00080.593-0.3480.66070.3227-0.50960.21880.41960.0506-0.01840.50860.05450.3368-26.591677.32368.8009
90.28580.19490.28275.05022.62211.72040.04550.1131-0.10450.3760.09580.09080.44760.0611-0.07710.4265-0.03420.00960.47430.02490.39-18.340362.83311.1107
104.612-1.8062-0.20873.47372.82112.5379-0.05570.0874-0.35530.8394-0.0284-0.25680.734-0.2131-0.22610.59580.01130.00990.5775-0.07240.6578-17.87149.80262.0167
116.9046-2.84681.40526.4536-2.2533.88520.41450.6833-0.0743-0.4726-0.38570.99270.4898-0.09070.1280.5178-0.1301-0.04550.4921-0.16060.5865-17.582653.52911.4208
121.2812-0.4295-1.99914.0862.9975.87970.3315-0.12260.0730.19370.2668-1.32280.0981.1747-0.59610.28690.0693-0.02870.76-0.0850.6635-11.579247.4293-5.5875
136.4021-3.5968-3.50617.59483.96136.5924-0.6142-0.7951-0.76470.92860.8745-0.52052.00870.96140.01470.69560.21290.03370.6514-0.02110.4732-13.043439.7238-0.618
145.4508-2.3457-3.70476.11183.34198.0061-1.301-0.2878-0.5061.60160.39711.02652.21360.58490.58870.96330.0010.11550.5210.10020.6925-20.517540.40643.6916
154.304-1.4267-0.62922.99550.53882.00780.1523-0.27240.1889-0.1403-0.86670.7403-0.14080.90090.20090.58610.01440.02130.5221-0.08670.4325-8.991526.797562.4003
163.5087-0.638-0.72153.46090.29011.2713-0.1891-0.34520.32050.52180.0932-0.1091-0.07640.1020.04370.503-0.0337-0.10790.4526-0.01130.36330.627325.784559.0162
173.4673-0.8963-0.30993.7851.42211.6843-0.1792-0.30960.6377-0.33230.20.0723-0.2686-0.08580.16420.47160.0357-0.04720.38980.03030.3274-8.228328.436756.9821
187.67991.50263.16610.22770.48121.7593-0.66170.43391.1524-0.12670.00970.5964-0.30150.45720.7670.6154-0.0245-0.10480.3775-0.01820.8674-36.875333.251546.2979
194.8021.08590.37223.49661.43282.8792-0.17270.01730.9257-0.0511-0.25530.9919-0.3296-0.25030.4190.56970.0212-0.11920.4315-0.00670.5853-33.881630.404148.068
203.34451.7583-0.0441.739-0.04960.0104-0.11310.77020.70270.1723-0.0960.9259-0.18030.03890.53390.60540.1132-0.15910.6319-0.13430.732-46.951530.646148.9969
217.01263.76841.81472.58041.44950.9617-0.4908-0.52630.7844-0.038-0.36661.07980.0874-0.2810.68060.50860.1381-0.08110.6693-0.0621.0418-40.770737.987654.9879
222.1046-1.00981.31134.2561-0.11485.5349-0.0490.4059-0.4075-0.1287-0.1502-0.23090.03520.54730.13710.27990.04220.11130.5690.02330.4694-57.231241.123417.5326
233.7701-4.4167-2.15965.91292.1383.8739-0.2532-0.1453-0.02030.27970.1207-0.07540.49950.17690.21580.4079-0.00380.06990.41270.08380.3894-56.547933.876720.1109
244.87591.5533-1.33544.7402-3.22466.2385-0.10990.6404-0.241-0.36680.29530.05451.0096-0.2427-0.14270.6211-0.0039-0.01460.5027-0.09180.46-61.47715.276127.6445
252.02311.15790.81636.2464-0.45044.3443-0.29150.40740.47680.50980.1318-0.1421-0.08280.3612-0.18050.4848-0.13610.05410.48550.01270.4096-56.862156.4653-4.5938
264.51330.53931.31333.94291.23877.53870.01930.2315-0.4704-0.19680.0483-0.68430.06510.5983-0.03550.3348-0.0404-0.00390.37690.05840.4297-57.367148.8169-10.4209
271.77510.2697-0.38020.46710.7681.6722-0.2699-0.11110.35260.494-0.2042-0.3837-1.2490.62810.00950.8281-0.546-0.10630.90070.51151.0836-41.954366.4003-11.8011
282.87770.0695-0.3053.7783-2.52763.45630.1910.13770.51510.8777-0.084-0.167-1.06570.2796-0.09970.7635-0.20490.07120.5480.06320.8553-43.618681.7135-26.7723
294.07851.34671.23791.69120.50671.73320.02220.17060.12170.0466-0.1-0.0113-0.1230.12940.07620.36510.00460.02070.35430.05250.26219.725316.598814.3648
302.90762.4411-0.51547.64620.04251.74920.2494-0.59260.46280.9217-0.3332-0.1976-0.11460.04760.04470.5652-0.0425-0.10580.5074-0.00950.45629.743130.959222.3552
312.9999-1.8902-0.58173.80321.54372.3580.60930.117-0.1503-0.5083-0.09460.1264-0.1675-0.0269-0.12140.4481-0.03780.0010.34430.00050.5435-13.040780.6779-13.5506
322.7046-0.90080.83372.78091.17051.7211-0.0204-0.16060.017-0.33890.16830.0087-0.127-0.1283-0.12030.3288-0.02740.03760.37670.04760.4311-13.060190.287-6.0833
333.1899-1.27720.30313.56130.56461.35010.0375-0.24530.4942-0.5809-0.1094-1.0249-0.47860.1659-0.21630.4705-0.06010.01140.5294-0.01980.5951-3.79690.3369-7.01
343.1092-1.74490.34223.63380.45221.7128-0.00610.19730.21050.1333-0.1843-0.4328-0.01080.4267-0.16260.3664-0.13050.01340.42130.04530.5521-7.004184.9681-11.4408
352.1956-0.5317-0.28172.52640.48951.5855-0.118-0.13810.14980.60270.14420.02060.2216-0.0314-0.05470.3713-0.0448-0.00230.41430.03460.4107-15.898284.3923-4.8477
361.80120.1296-0.02854.77240.99443.6130.1658-0.1079-0.45750.0773-0.08011.04280.9189-0.6168-0.0510.5717-0.1487-0.17540.542-0.00230.8097-21.822748.9761-11.0207
371.07410.8358-0.92784.93770.59644.64040.2431-0.3662-0.2494-0.2885-0.18460.54840.3802-0.5347-0.15570.333-0.066-0.05140.4454-0.04680.634-20.72158.4345-11.2418
380.41130.1828-0.80794.56080.49553.6332-0.04820.31780.0827-0.57130.21520.91720.5051-0.4645-0.09470.5596-0.0631-0.19030.5737-0.04040.6592-23.347355.4691-20.7466
394.6460.15221.49112.60050.12261.01270.0596-0.0859-0.1236-0.084-0.0063-0.1185-0.2325-0.151-0.01820.4626-0.0048-0.01970.37710.00870.2472-1.47814.339840.6553
404.6157-0.8348-0.06242.7870.84664.09640.05730.57310.8852-0.8119-0.07730.4071-1.0496-0.1791-0.03970.713-0.0184-0.09040.6160.17970.7761-30.028435.019834.7221
411.42170.57090.60054.8938-0.15951.08420.1746-0.4407-0.28080.4666-0.2157-0.4206-0.331-0.11540.02650.404-0.00620.07680.40430.01650.4131-65.798237.089543.5193
422.62920.78080.18164.2483-1.00671.1268-0.03780.02240.1940.0190.16550.20820.1081-0.04-0.01360.2634-0.01860.03820.45450.00730.278-68.298446.263336.1427
431.79330.78150.00144.2139-0.643-0.0085-0.07220.10260.14510.02920.17850.39770.14270.1658-0.04340.43680.0570.06440.4186-0.04960.3675-72.637141.576738.6071
441.4344-0.54360.5387.2915-1.41771.670.09220.1285-0.2439-0.3101-0.0605-0.24210.28350.14190.02840.31970.08430.00080.4846-0.00330.2282-60.339224.959135.6469
452.98552.577-1.13482.82630.31433.6790.03810.0870.0538-0.35370.2585-0.2931-0.16540.5847-0.26830.6122-0.0304-0.11270.3975-0.05410.5147-51.630914.995141.8229
463.13882.8191-0.39423.09990.14523.880.19070.0956-0.40160.3855-0.0166-0.3360.43020.1154-0.10530.51470.0568-0.00080.375-0.02390.4385-55.02439.477742.6602
472.18170.5406-0.97316.8123-1.82252.6736-0.14021.00070.6444-0.46610.0797-0.9670.611-0.22180.00480.4168-0.13050.05050.5086-0.08020.3934-64.835655.2117-34.218
482.42660.6699-0.98115.6765-2.18381.68170.1022-0.0390.04190.0273-0.01610.0657-0.06080.2882-0.14250.3105-0.0179-0.05180.3831-0.01540.2819-70.637147.2165-27.0437
493.22080.1661-0.13676.6388-2.10381.64750.0475-0.00870.2167-0.11180.17870.31560.17320.0027-0.2350.3719-0.1331-0.02580.32010.03950.2819-72.084653.6003-32.2129
502.56590.1885-0.46942.57980.76450.3901-0.2475-0.2483-0.31960.54030.1011-0.60070.0809-0.01680.15930.43530.0159-0.07180.45880.02170.3907-63.134545.9653-23.02
511.34880.9234-2.14474.2937-0.722.1068-0.4854-0.51410.4783-0.29620.0772-0.7205-0.2470.51910.02180.5308-0.07210.11740.55140.13190.7483-46.804674.4664-36.0553
523.23072.5039-1.53156.1919-0.43624.22850.08-0.16180.075-0.4549-0.0503-0.85930.06410.4398-0.00190.40320.00860.09820.4860.12320.5855-47.781468.4629-33.4178
536.09082.6775-3.66726.2127-1.22493.97090.12570.107-0.0076-1.0706-0.3109-1.03020.3125-00.06590.729-0.08620.13990.6840.16760.5885-45.623767.2878-43.3585
541.35222.90390.60656.3039-0.34434.93080.13670.4873-0.3083-0.4434-0.04130.28210.91080.3586-0.06720.72010.2392-0.14430.6639-0.12910.5912.615875.02995.582
551.21691.8806-0.8814.6171-1.99221.321-0.03320.2267-0.7136-0.2876-0.2569-0.26930.601-0.06440.28180.97170.1255-0.17390.7499-0.21570.907610.554962.821414.6557
562.98341.8672-1.94672.2593-1.3613.076-0.86240.755-0.5189-0.51390.630.21780.3005-0.71550.1230.958-0.0116-0.04420.7333-0.12521.236-4.143346.810921.3425
577.36122.6791-3.73482.6088-1.83953.7506-1.8982.1233-0.9039-2.18641.8306-0.36850.4595-1.03540.88471.9961-0.1543-0.1960.5638-0.08541.1493-1.070138.139715.1909
584.397-0.56610.32962.56010.34223.06090.23950.2723-0.61960.0235-0.07310.02030.39530.1414-0.15780.40890.0621-0.05910.3146-0.06830.43218.180783.037827.4724
592.23370.5599-0.03410.4002-1.07332.19410.2356-0.2187-1.2875-0.3024-0.1480.73160.73020.2355-0.15351.0621-0.0199-0.38210.66750.16491.83495.931949.739734.1206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 150 )
4X-RAY DIFFRACTION4chain 'A' and (resid 151 through 186 )
5X-RAY DIFFRACTION5chain 'A' and (resid 187 through 211 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 18 )
7X-RAY DIFFRACTION7chain 'C' and (resid 19 through 75 )
8X-RAY DIFFRACTION8chain 'C' and (resid 76 through 90 )
9X-RAY DIFFRACTION9chain 'C' and (resid 91 through 128 )
10X-RAY DIFFRACTION10chain 'C' and (resid 129 through 150 )
11X-RAY DIFFRACTION11chain 'C' and (resid 151 through 172 )
12X-RAY DIFFRACTION12chain 'C' and (resid 173 through 186 )
13X-RAY DIFFRACTION13chain 'C' and (resid 187 through 198 )
14X-RAY DIFFRACTION14chain 'C' and (resid 199 through 211 )
15X-RAY DIFFRACTION15chain 'E' and (resid 1 through 18 )
16X-RAY DIFFRACTION16chain 'E' and (resid 19 through 75 )
17X-RAY DIFFRACTION17chain 'E' and (resid 76 through 113 )
18X-RAY DIFFRACTION18chain 'E' and (resid 114 through 150 )
19X-RAY DIFFRACTION19chain 'E' and (resid 151 through 186 )
20X-RAY DIFFRACTION20chain 'E' and (resid 187 through 197 )
21X-RAY DIFFRACTION21chain 'E' and (resid 198 through 211 )
22X-RAY DIFFRACTION22chain 'I' and (resid 1 through 75 )
23X-RAY DIFFRACTION23chain 'I' and (resid 76 through 113 )
24X-RAY DIFFRACTION24chain 'I' and (resid 114 through 211 )
25X-RAY DIFFRACTION25chain 'K' and (resid 1 through 25 )
26X-RAY DIFFRACTION26chain 'K' and (resid 26 through 102 )
27X-RAY DIFFRACTION27chain 'K' and (resid 103 through 113 )
28X-RAY DIFFRACTION28chain 'K' and (resid 114 through 211 )
29X-RAY DIFFRACTION29chain 'B' and (resid 1 through 145 )
30X-RAY DIFFRACTION30chain 'B' and (resid 146 through 213 )
31X-RAY DIFFRACTION31chain 'D' and (resid 1 through 17 )
32X-RAY DIFFRACTION32chain 'D' and (resid 18 through 59 )
33X-RAY DIFFRACTION33chain 'D' and (resid 60 through 72 )
34X-RAY DIFFRACTION34chain 'D' and (resid 73 through 87 )
35X-RAY DIFFRACTION35chain 'D' and (resid 88 through 119 )
36X-RAY DIFFRACTION36chain 'D' and (resid 120 through 145 )
37X-RAY DIFFRACTION37chain 'D' and (resid 146 through 188 )
38X-RAY DIFFRACTION38chain 'D' and (resid 189 through 213 )
39X-RAY DIFFRACTION39chain 'F' and (resid 1 through 111 )
40X-RAY DIFFRACTION40chain 'F' and (resid 112 through 213 )
41X-RAY DIFFRACTION41chain 'J' and (resid 1 through 17 )
42X-RAY DIFFRACTION42chain 'J' and (resid 18 through 59 )
43X-RAY DIFFRACTION43chain 'J' and (resid 60 through 95 )
44X-RAY DIFFRACTION44chain 'J' and (resid 96 through 145 )
45X-RAY DIFFRACTION45chain 'J' and (resid 146 through 165 )
46X-RAY DIFFRACTION46chain 'J' and (resid 166 through 213 )
47X-RAY DIFFRACTION47chain 'L' and (resid 1 through 17 )
48X-RAY DIFFRACTION48chain 'L' and (resid 18 through 72 )
49X-RAY DIFFRACTION49chain 'L' and (resid 73 through 87 )
50X-RAY DIFFRACTION50chain 'L' and (resid 88 through 111 )
51X-RAY DIFFRACTION51chain 'L' and (resid 112 through 145 )
52X-RAY DIFFRACTION52chain 'L' and (resid 146 through 188 )
53X-RAY DIFFRACTION53chain 'L' and (resid 189 through 213 )
54X-RAY DIFFRACTION54chain 'G' and (resid 1 through 38 )
55X-RAY DIFFRACTION55chain 'G' and (resid 39 through 150 )
56X-RAY DIFFRACTION56chain 'G' and (resid 151 through 197 )
57X-RAY DIFFRACTION57chain 'G' and (resid 198 through 211 )
58X-RAY DIFFRACTION58chain 'H' and (resid 1 through 119 )
59X-RAY DIFFRACTION59chain 'H' and (resid 120 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