[English] 日本語
Yorodumi
- PDB-4plk: Hepatitis E Virus E2s domain (Genotype I) in complex with a neutr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4plk
TitleHepatitis E Virus E2s domain (Genotype I) in complex with a neutralizing antibody 8G12
Components
  • 8G12 heavy chain
  • 8G12 light chain
  • Capsid protein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Complex / neutralizing antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral capsid / host cell surface / host cell cytoplasm / structural molecule activity / RNA binding / cytoplasm
Similarity search - Function
Hepatitis E virus structural protein 2 / Structural protein 2 nucleoplasmin-like domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHepatitis E virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsTang, X.H. / Li, S.W. / Sivaraman, J.
CitationJournal: Cell Res. / Year: 2015
Title: Structural basis for the neutralization of hepatitis E virus by a cross-genotype antibody
Authors: Gu, Y. / Tang, X. / Zhang, X. / Song, C. / Zheng, M. / Wang, K. / Zhang, J. / Ng, M.H. / Hew, C.L. / Li, S. / Xia, N. / Sivaraman, J.
History
DepositionMay 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
L: 8G12 light chain
H: 8G12 heavy chain
C: 8G12 light chain
D: 8G12 heavy chain
E: Capsid protein
F: Capsid protein
K: 8G12 light chain
J: 8G12 heavy chain
G: 8G12 light chain
I: 8G12 heavy chain


Theoretical massNumber of molelcules
Total (without water)255,24812
Polymers255,24812
Non-polymers00
Water00
1
A: Capsid protein
B: Capsid protein
L: 8G12 light chain
H: 8G12 heavy chain
C: 8G12 light chain
D: 8G12 heavy chain


Theoretical massNumber of molelcules
Total (without water)127,6246
Polymers127,6246
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Capsid protein
F: Capsid protein
K: 8G12 light chain
J: 8G12 heavy chain
G: 8G12 light chain
I: 8G12 heavy chain


Theoretical massNumber of molelcules
Total (without water)127,6246
Polymers127,6246
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.196, 191.993, 192.584
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Capsid protein


Mass: 15607.430 Da / Num. of mol.: 4 / Fragment: E2s domain, UNP residues 8-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis E virus / Production host: Escherichia coli (E. coli) / References: UniProt: L0L7P5
#2: Antibody
8G12 light chain


Mass: 23415.779 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody
8G12 heavy chain


Mass: 24788.795 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 69.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: 12% PEG 5000, 0.05M NaH2PO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→33.992 Å / Num. obs: 31821 / % possible obs: 90.5 % / Redundancy: 3.2 % / Net I/σ(I): 5.8

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→33.992 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2961 1879 6.2 %Random
Rwork0.264 ---
obs0.2662 30302 91.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4→33.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17368 0 0 0 17368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00617803
X-RAY DIFFRACTIONf_angle_d1.5824286
X-RAY DIFFRACTIONf_dihedral_angle_d14.9496268
X-RAY DIFFRACTIONf_chiral_restr0.0652748
X-RAY DIFFRACTIONf_plane_restr0.0063086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.1080.35981280.34471959X-RAY DIFFRACTION83
4.108-4.22870.33091350.32481959X-RAY DIFFRACTION82
4.2287-4.36490.34651340.30751991X-RAY DIFFRACTION84
4.3649-4.52050.28121510.27182077X-RAY DIFFRACTION85
4.5205-4.70110.32281400.28652018X-RAY DIFFRACTION87
4.7011-4.91440.28721410.27852137X-RAY DIFFRACTION88
4.9144-5.17270.31251430.26722138X-RAY DIFFRACTION91
5.1727-5.49550.32691550.25222251X-RAY DIFFRACTION93
5.4955-5.91780.34531410.2722341X-RAY DIFFRACTION97
5.9178-6.50960.34091450.27942362X-RAY DIFFRACTION98
6.5096-7.44290.24181630.27692367X-RAY DIFFRACTION99
7.4429-9.34490.26951590.24342403X-RAY DIFFRACTION99
9.3449-33.99320.25011440.20092420X-RAY DIFFRACTION98
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)
13.6388-1.14920.46732.3615-2.26893.9346-0.7501-0.27331.8063-0.2546-0.6929-0.3401-1.0944-0.14530.151.2846-0.06350.38850.4658-0.5652.866413.3927-3.870891.4268
24.79391.14392.44262.38870.72544.41290.8541-1.26280.2042-0.51450.3160.50930.709-0.88810.23070.2735-0.09150.09720.86940.10231.73077.5585-23.008689.6853
32.88590.040.52963.6505-1.54950.8650.9325-0.33840.3891-0.29210.17921.34620.48490.0095-0.08280.5239-0.3048-0.09651.16390.40451.38273.5113-24.278683.2285
42.65562.28560.52692.2933-0.37222.17850.2248-1.80311.27620.7263-0.57351.1742-1.0501-0.2127-0.1931.5509-0.0840.37581.06090.16691.58911.0717-9.754896.5659
52.3873-1.6340.43653.5549-1.28182.4654-0.0279-0.1160.73940.99530.58221.11290.3248-0.7775-0.38971.42320.36130.18350.24830.15132.44922.0848-6.980588.6657
64.92970.75080.55115.6239-0.60733.3441-0.58140.05811.7043-1.0177-0.2291.5048-0.3377-0.6096-0.05511.44070.49410.1111.65060.49121.39645.6195-7.371877.5897
75.08060.30550.32473.1068-1.10482.60790.0306-0.24680.51-0.96110.37680.86981.135-0.3258-0.34090.72970.06120.28061.11370.42941.144310.5863-20.565484.1921
84.8009-0.01960.70322.179-1.00093.64180.47740.59910.686-0.6862-0.16890.40430.77570.1564-0.3594-0.2909-1.0094-0.09211.53980.65570.996816.9562-27.529276.3281
91.65580.42990.55482.352-0.06972.88650.67160.71480.5139-0.93320.681.56370.91581.82320.35480.249-0.6780.20050.03240.97511.61385.9002-23.199383.7432
100.70260.9024-1.28811.0145-1.79356.62110.0278-0.2270.97830.29360.29561.283-1.34450.5376-0.12680.78150.060.10.80320.24561.544114.8066-13.791784.336
112.92291.00070.21580.9979-0.57550.67440.178-1.43781.14720.82-0.2990.254-0.7921-0.62810.24721.2313-0.845-0.13752.9395-0.62910.854626.9585-15.7052102.6287
122.9144-1.7509-1.27071.13580.91010.71010.6222-0.5707-0.3297-0.1616-1.7677-0.98420.63040.2469-0.0342-1.60950.22421.06141.99450.24670.564835.2678-22.922381.8112
136.827-1.14731.48862.3954-1.27342.55460.1294-2.09430.92770.3726-0.0698-0.9703-1.39221.40120.13380.8935-0.31610.00531.9060.31450.896834.7353-13.85592.0083
140.63420.41520.38915.7353-2.4723.5263-0.2839-0.3105-0.81620.84150.48540.2990.5686-0.5376-0.10381.2467-0.32860.14791.48370.03331.00734.0763-22.3041103.8585
151.15821.54230.07622.40380.13440.12260.357-0.0114-0.6201-0.0441-0.3303-1.04051.20980.31030.31530.7973-0.0493-0.08461.71160.42921.085134.4833-28.862192.2887
166.14841.20751.08010.8328-0.08832.04230.14011.36660.00860.6806-0.7289-0.02610.46580.66490.60840.4409-0.17020.27641.61370.10061.115624.5205-22.483378.3521
171.8197-1.7819-1.23051.73410.79732.46421.1754-1.4670.8533-0.26750.1858-1.0219-0.43561.37960.4927-1.8741.0239-1.93141.55911.6405-0.841835.3539-24.703289.3306
181.42840.6668-0.83212.19390.0740.69130.1862-0.8382-0.2472-0.2344-0.2161-0.47320.15420.2598-0.24910.4987-0.01020.05111.4050.2030.823329.1295-21.839183.1578
191.6882-1.7242.67944.8428-4.21475.41291.11350.5750.094-1.2916-0.91790.44240.92821.20430.14941.40970.39020.42891.30210.12671.361114.282-59.647493.0345
200.72051.3818-0.14424.6038-0.65150.5439-0.40450.5118-0.0672-1.5659-0.4408-0.13830.53910.8161-0.14320.94030.90630.0173-0.11221.80890.352218.4822-48.386290.8363
211.88972.3044-2.11853.1544-3.32364.0625-0.5252-0.2646-0.95321.13880.15010.1261.10690.44570.92840.92320.07110.30821.00550.84262.491111.0757-54.2985105.2847
220.23570.2219-1.23342.4826-0.75438.8698-0.0194-0.6855-0.31330.92030.17250.4885-1.17511.32930.36441.21470.99530.61371.81511.52612.026322.9995-52.8297100.1658
231.76110.7680.36683.395-1.72422.39610.7258-1.9399-1.6457-0.05660.169-1.24051.16150.95040.28952.14350.84080.58961.3941.53361.1415.1663-62.1211103.5892
241.9238-1.61960.05565.03560.68043.1315-0.8673-0.70880.0479-1.1811.0623-1.1520.92350.80450.41720.44630.09160.15790.92580.46811.266611.0522-43.928594.1911
250.81310.95490.6873.24250.80930.4966-1.003-0.5658-0.6879-0.2789-0.4652-0.42562.15930.56260.26032.45120.32680.52411.12570.76812.29710.2737-73.2649102.2175
261.1471-0.0988-0.92341.14621.19421.8051-1.01140.55850.17541.1993-0.4728-0.4581-0.1670.64481.13251.1895-0.05520.0241.38560.39021.584-16.9266-77.9051115.8672
272.1968-0.3965-0.96530.74650.48052.9928-0.46310.3259-1.9989-0.266-0.3124-1.59641.1168-0.35850.29442.3448-0.09510.56951.57030.84692.2514-9.4311-77.6248104.9419
282.23950.9766-0.94370.4877-0.52120.56290.4497-0.1853-0.252-0.8264-0.4363-0.21150.38850.35730.31823.5739-0.48431.9999-0.52091.13133.7728-13.9302-88.1883107.917
293.69821.3793-2.15683.0522-1.47922.1090.2619-1.8357-0.25010.69010.40170.77560.46920.9825-0.23120.6571-0.17320.31451.39480.22591.2623-1.3915-42.795107.6794
304.4182-0.2121-2.35884.4306-1.62553.46770.3367-0.70131.75241.2707-0.43150.05170.00270.38090.26370.5483-0.23860.46270.23630.26132.28753.6071-34.2704101.1702
312.80792.0807-1.54412.1137-1.2552.27090.3396-1.4080.3878-0.0186-0.41480.27090.53240.339-0.0380.77020.10570.16571.29660.43541.676-2.9819-46.2703105.6329
326.8738-5.64875.04639.0732-4.29748.4110.24080.0038-0.4338-0.22640.0211-0.7140.36450.8665-0.15841.3769-0.01110.18081.44450.27561.4784-10.105-72.3532116.1179
336.0783-3.30065.03734.3746-1.72125.54990.6625-0.30920.84160.9175-0.2298-0.90670.45930.4555-0.24381.1096-0.14830.2761.38910.49961.7765-5.1027-64.474117.7693
341.14961.01762.21647.8729-4.17049.63360.303-0.36360.5671-1.1566-0.682-1.07060.94321.40480.42131.1140.0850.27091.26990.10071.675-10.6179-69.2276119.0745
350.4489-0.31770.23280.4292-0.98564.3531-0.4110.9670.1775-0.8756-0.19880.40640.93240.31960.3121.4682-0.49-0.31951.6520.20730.931624.468-15.387152.3901
363.95313.6339-4.193.3549-3.78574.85720.23151.69890.9644-0.8430.23910.455-0.5706-0.9137-0.34710.2949-0.68970.21142.75561.17591.227228.5359-2.187753.3913
371.5617-0.6863-1.90493.2167-1.69664.60940.38990.53490.6845-1.22910.40851.4533-0.3808-0.5447-0.7010.9771-0.5381-0.42511.87810.68961.526622.8537-7.653.5622
380.21330.1301-0.27770.0123-0.50470.2339-1.0884-0.6295-0.9742-0.90110.2001-0.68810.3630.10680.23772.0074-0.5252-0.08582.51890.86341.560546.13222.423730
391.28810.41091.59541.87290.24961.836-0.29260.36-1.2729-1.54430.77810.49830.8033-0.4974-0.59432.5943-0.8072-0.08872.35080.72131.77150.4285-3.606229.3341
40-0.0115-0.131-0.01842.86320.3126-0.0571-0.14530.9372-0.5364-1.93690.079-1.01770.51450.9257-0.14282.708-0.6650.30542.6088-0.08730.942558.36581.117617.799
414.90512.3282-2.12623.5817-2.27085.51520.4668-1.19750.7631-0.2103-0.20990.5011-0.64620.8879-0.23550.7611-0.2249-0.00891.39410.31571.11640.3049-2.377266.1557
420.37680.4933-0.27993.28570.48691.01450.99780.3136-0.7917-0.69880.51240.1537-0.56220.3642-0.94851.2154-0.20370.17742.06910.25971.582654.38968.686736.1352
430.35580.6345-1.15223.8556-3.03286.7147-0.2080.31560.356-0.56280.59750.8370.4053-1.9325-0.10811.4455-0.33760.03912.03820.52091.187650.112311.275638.5301
443.92240.89961.98586.1601-2.4612.40680.58011.6435-0.9594-2.34890.17550.7351-0.83460.24580.58721.3790.61240.01312.2628-0.2420.814454.543-100.901-6.6568
456.03510.09333.73733.07360.40233.64480.30340.5278-0.62551.217-1.4671-0.9484-0.81440.4404-0.2017-0.47130.3782-0.22951.96880.16080.741160.1587-99.856212.4132
462.6689-0.9712-1.08911.2336-0.68181.79970.4920.2813-0.19030.9174-1.052-0.2290.1581.63820.07110.52440.1736-0.32761.33660.35920.9364.2236-93.407513.81
474.44993.18385.24954.55344.5397.18250.5951.4269-2.2617-0.991-0.11271.33850.50660.1464-0.88521.33890.3261-0.47361.3623-0.21291.373956.8908-106.7021-0.856
481.02081.10951.93925.75943.39644.2084-0.44361.6384-0.4415-0.0352-0.0275-0.65290.5845-0.371-0.33940.90860.35270.05162.663-0.07480.745465.9044-98.7453-3.8089
494.6195-0.0565-2.21843.6980.52773.3841-0.3241.8530.3512-0.49780.6968-0.3985-1.28010.7636-0.37881.29980.28410.42.51120.42831.527162.4928-87.1002-2.7672
503.368-0.9138-0.06741.2608-0.29053.62510.07951.25450.0909-1.1797-0.622-0.5893-0.66031.9704-0.4576-2.52090.836-0.66032.02980.64521.068157.0997-94.329510.1989
510.137-0.2432-0.14693.7976-1.61922.09810.51360.85090.591-0.0187-0.03981.1883-0.55670.1164-0.18080.85620.0061-0.27751.27410.47131.437450.7045-86.647317.1764
520.20070.41550.00170.8268-0.2291.19960.41221.35271.04240.439-0.20650.8591-0.58240.8240.59270.06050.3096-0.59552.12450.75071.025261.7458-93.874212.6003
531.7523-1.51240.58125.44411.461.8881-0.37171.0634-0.6999-0.9812-0.54930.01870.02450.35270.86820.5888-0.0036-0.07871.90850.18180.558552.9156-94.19413.4169
540.55670.8484-0.15492.9441-1.30130.72650.370.8694-1.2605-0.17680.1772-1.57851.9811.1353-0.69811.00090.5316-0.74121.2813-0.75912.351140.5222-113.14595.4836
550.9618-0.5652-0.6450.32110.27790.61560.3971-0.1119-0.67121.07511.03361.129-0.7548-0.7333-0.43690.2910.28490.21111.19990.39741.958732.4646-91.91612.3606
565.5426-0.40211.88163.0875-2.54473.8067-0.09880.9567-1.8851-0.81940.99441.72741.0579-1.2921-0.53360.66740.0956-0.12071.10270.12761.287332.9065-102.23883.3578
570.395-0.15620.05341.3023-1.30081.41070.405-0.1678-1.3392-0.09250.336-0.55210.24920.37760.11091.0195-0.1227-0.16541.20180.22652.702433.6243-113.907112.2089
586.3716-1.1054-0.10182.8065-0.43513.51170.5944-0.9238-0.98041.16150.4331.1853-0.7803-1.451-0.43450.6289-0.038-0.23921.16570.55931.745133.207-102.259218.3943
593.26980.16940.21663.27970.45787.62690.17440.4830.69470.36951.16321.55290.02380.3478-0.80510.50960.24020.1781.07620.11171.247943.1428-88.529612.0166
601.3149-1.1725-0.39851.0650.5070.74810.5815-1.0156-1.18280.5815-0.23911.4698-0.06-0.2145-0.38680.6119-0.0171-0.00280.98260.26261.563635.7258-96.270412.7617
613.48921.637-0.17035.1179-3.20193.65070.2648-0.71660.5555-0.29510.27420.9401-0.15140.515-0.32981.55120.32690.14781.0455-0.00751.336953.2934-103.002849.2231
623.8803-2.19481.01564.5294-0.96031.7089-0.0775-2.43510.46790.5680.7448-0.6039-0.18940.1027-0.66191.04360.37720.25811.65490.56481.022552.9684-107.844240.9634
634.2786-1.15980.39535.2562-1.56872.7057-0.4542-1.0345-1.16950.54330.91432.11950.70360.0574-0.57571.25430.44230.68861.24221.292.070544.6182-110.42142.4423
643.087-3.35823.89385.5508-2.96395.78870.6503-0.9713-1.94650.0339-0.3790.08470.809-0.9895-0.29771.49270.32920.03781.64310.91831.362752.3121-113.461551.8632
651.96710.6517-1.45240.3298-0.25063.1724-0.4374-0.62690.10740.84-0.51220.3379-0.41610.0209-0.43640.78690.23240.49411.4640.70511.994757.3368-104.247833.8148
660.97860.10651.27950.1003-0.2222.5121-1.5227-0.1294-0.82661.69660.69840.2064-0.62260.39970.44072.73180.36740.57922.44120.87820.958356.972-112.180663.1485
674.7362-1.7456-0.03641.23790.73820.8861-0.57150.10220.03640.47410.95480.3815-0.87930.71320.2911.6499-0.3714-0.43632.76880.64651.586984.6897-126.236267.3446
681.8951-0.4226-0.2522.14550.60470.35060.7254-1.81940.19230.03040.0737-0.251-0.5269-0.90510.24712.9530.5466-0.25222.40590.87231.309876.741-115.180367.0917
695.7562-2.32212.19621.7689-0.49171.36030.1668-1.1935-0.9571.28360.020.3965-1.04890.8121-0.92322.98930.7189-0.35552.74090.49981.220481.2797-117.669177.6353
704.3677-1.70131.68092.4049-1.01381.96130.1017-0.116-1.7382-0.0153-0.05670.0985-0.06160.6802-0.19340.86680.41440.04571.37370.60941.209769.0302-117.778132.3427
712.4245-1.21270.57161.7392-0.25391.30050.36281.32730.1193-0.4505-0.0670.65130.791-0.105-0.30140.61370.46390.0791.67550.37151.34664.1352-111.229723.9148
722.3017-0.65021.67722.8451-1.61873.99880.02810.3728-0.6799-0.02570.23670.41740.41450.2845-0.32380.7390.1770.10031.41450.52821.229670.6524-115.790335.7343
738.375.7198-7.68897.254-4.7867.75570.4479-0.5231-0.465-0.4336-0.05251.2381-0.0776-0.6846-0.3031.885-0.0072-0.15281.52640.59071.495877.8191-126.258661.7713
744.08844.0696-0.70345.966-2.1324.35970.1862-0.5445-1.18311.0364-0.0480.31560.1227-0.7177-0.66751.26450.3627-0.26732.00330.59781.595972.8075-128.083454.0859
750.8162-0.87322.39234.0658-0.89627.82110.0988-0.1744-1.33770.31710.34080.4333-0.0335-0.427-0.37971.24370.403-0.0781.79850.62071.618778.3829-129.200358.7336
760.77470.71730.23274.6601-0.62142.7538-0.22020.39920.63560.4874-0.0631-0.9263-0.42720.36350.31651.3937-0.3248-0.37881.33860.1821.593542.9989-62.46354.8126
772.6403-0.01740.94233.9691-1.11133.2399-0.3731-0.19961.2036-0.6273-0.4052-0.2774-0.89710.27850.42390.8809-0.1488-0.25961.17210.77871.744439.3412-63.6123-8.2127
785.14032.3622-3.41163.3854-1.60912.06370.0521.57781.0661-0.1149-0.6515-0.4604-1.03581.65330.27661.0019-0.3995-0.47391.78960.8211.530744.8397-63.6789-2.8408
790.0789-0.1410.14160.1501-0.01940.1927-0.56470.70.45810.41490.1987-0.0769-0.96640.2360.35111.9167-0.0818-0.56911.22360.71882.74221.4632-40.5251-13.1353
800.66980.65160.73910.90021.15032.32850.1077-1.8309-0.81981.21670.2727-0.6736-1.0526-0.17260.0922.4611-0.0568-0.36491.39030.5292.286715.7035-36.9629-8.0944
815.0089-2.04681.44994.5788-1.44273.05930.44791.2355-0.6024-0.6564-0.2110.4509-0.18020.27330.00990.77840.0614-0.33441.41440.26961.319127.39-76.4202-8.2358
821.45710.3004-1.50490.83831.60454.87190.76120.31250.0718-0.4854-0.462-0.0257-0.9629-0.1520.49191.27130.2063-0.381.36650.75882.03913.3021-46.462-19.4489
83-0.0460.0615-0.00016.6562-3.8791.90430.29020.68-0.06010.2562-0.8525-0.8336-0.39311.07570.30261.26530.0266-0.26731.45680.58041.946517.696-48.797-21.8042
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 459 through 469 )
2X-RAY DIFFRACTION2chain 'A' and (resid 470 through 481 )
3X-RAY DIFFRACTION3chain 'A' and (resid 482 through 501 )
4X-RAY DIFFRACTION4chain 'A' and (resid 502 through 511 )
5X-RAY DIFFRACTION5chain 'A' and (resid 512 through 521 )
6X-RAY DIFFRACTION6chain 'A' and (resid 522 through 531 )
7X-RAY DIFFRACTION7chain 'A' and (resid 532 through 554 )
8X-RAY DIFFRACTION8chain 'A' and (resid 555 through 564 )
9X-RAY DIFFRACTION9chain 'A' and (resid 565 through 594 )
10X-RAY DIFFRACTION10chain 'A' and (resid 595 through 605 )
11X-RAY DIFFRACTION11chain 'B' and (resid 459 through 469 )
12X-RAY DIFFRACTION12chain 'B' and (resid 470 through 491 )
13X-RAY DIFFRACTION13chain 'B' and (resid 492 through 515 )
14X-RAY DIFFRACTION14chain 'B' and (resid 516 through 525 )
15X-RAY DIFFRACTION15chain 'B' and (resid 526 through 545 )
16X-RAY DIFFRACTION16chain 'B' and (resid 546 through 563 )
17X-RAY DIFFRACTION17chain 'B' and (resid 564 through 582 )
18X-RAY DIFFRACTION18chain 'B' and (resid 583 through 605 )
19X-RAY DIFFRACTION19chain 'L' and (resid 1 through 18 )
20X-RAY DIFFRACTION20chain 'L' and (resid 19 through 34 )
21X-RAY DIFFRACTION21chain 'L' and (resid 35 through 48 )
22X-RAY DIFFRACTION22chain 'L' and (resid 49 through 75 )
23X-RAY DIFFRACTION23chain 'L' and (resid 76 through 88 )
24X-RAY DIFFRACTION24chain 'L' and (resid 89 through 101 )
25X-RAY DIFFRACTION25chain 'L' and (resid 102 through 113 )
26X-RAY DIFFRACTION26chain 'L' and (resid 114 through 128 )
27X-RAY DIFFRACTION27chain 'L' and (resid 129 through 187 )
28X-RAY DIFFRACTION28chain 'L' and (resid 188 through 212 )
29X-RAY DIFFRACTION29chain 'H' and (resid 1 through 42 )
30X-RAY DIFFRACTION30chain 'H' and (resid 43 through 58 )
31X-RAY DIFFRACTION31chain 'H' and (resid 59 through 144 )
32X-RAY DIFFRACTION32chain 'H' and (resid 145 through 155 )
33X-RAY DIFFRACTION33chain 'H' and (resid 156 through 175 )
34X-RAY DIFFRACTION34chain 'H' and (resid 176 through 223 )
35X-RAY DIFFRACTION35chain 'C' and (resid 1 through 33 )
36X-RAY DIFFRACTION36chain 'C' and (resid 34 through 49 )
37X-RAY DIFFRACTION37chain 'C' and (resid 50 through 101 )
38X-RAY DIFFRACTION38chain 'C' and (resid 102 through 139 )
39X-RAY DIFFRACTION39chain 'C' and (resid 140 through 186 )
40X-RAY DIFFRACTION40chain 'C' and (resid 187 through 211 )
41X-RAY DIFFRACTION41chain 'D' and (resid 1 through 119 )
42X-RAY DIFFRACTION42chain 'D' and (resid 120 through 145 )
43X-RAY DIFFRACTION43chain 'D' and (resid 146 through 223 )
44X-RAY DIFFRACTION44chain 'E' and (resid 459 through 469 )
45X-RAY DIFFRACTION45chain 'E' and (resid 470 through 481 )
46X-RAY DIFFRACTION46chain 'E' and (resid 482 through 501 )
47X-RAY DIFFRACTION47chain 'E' and (resid 502 through 511 )
48X-RAY DIFFRACTION48chain 'E' and (resid 512 through 521 )
49X-RAY DIFFRACTION49chain 'E' and (resid 522 through 531 )
50X-RAY DIFFRACTION50chain 'E' and (resid 532 through 554 )
51X-RAY DIFFRACTION51chain 'E' and (resid 555 through 564 )
52X-RAY DIFFRACTION52chain 'E' and (resid 565 through 594 )
53X-RAY DIFFRACTION53chain 'E' and (resid 595 through 605 )
54X-RAY DIFFRACTION54chain 'F' and (resid 459 through 469 )
55X-RAY DIFFRACTION55chain 'F' and (resid 470 through 491 )
56X-RAY DIFFRACTION56chain 'F' and (resid 492 through 515 )
57X-RAY DIFFRACTION57chain 'F' and (resid 516 through 525 )
58X-RAY DIFFRACTION58chain 'F' and (resid 526 through 545 )
59X-RAY DIFFRACTION59chain 'F' and (resid 546 through 563 )
60X-RAY DIFFRACTION60chain 'F' and (resid 564 through 605 )
61X-RAY DIFFRACTION61chain 'K' and (resid 1 through 18 )
62X-RAY DIFFRACTION62chain 'K' and (resid 19 through 48 )
63X-RAY DIFFRACTION63chain 'K' and (resid 49 through 75 )
64X-RAY DIFFRACTION64chain 'K' and (resid 76 through 88 )
65X-RAY DIFFRACTION65chain 'K' and (resid 89 through 101 )
66X-RAY DIFFRACTION66chain 'K' and (resid 102 through 113 )
67X-RAY DIFFRACTION67chain 'K' and (resid 114 through 128 )
68X-RAY DIFFRACTION68chain 'K' and (resid 129 through 187 )
69X-RAY DIFFRACTION69chain 'K' and (resid 188 through 212 )
70X-RAY DIFFRACTION70chain 'J' and (resid 1 through 42 )
71X-RAY DIFFRACTION71chain 'J' and (resid 43 through 58 )
72X-RAY DIFFRACTION72chain 'J' and (resid 59 through 144 )
73X-RAY DIFFRACTION73chain 'J' and (resid 145 through 155 )
74X-RAY DIFFRACTION74chain 'J' and (resid 156 through 175 )
75X-RAY DIFFRACTION75chain 'J' and (resid 176 through 223 )
76X-RAY DIFFRACTION76chain 'G' and (resid 1 through 33 )
77X-RAY DIFFRACTION77chain 'G' and (resid 34 through 49 )
78X-RAY DIFFRACTION78chain 'G' and (resid 50 through 101 )
79X-RAY DIFFRACTION79chain 'G' and (resid 102 through 139 )
80X-RAY DIFFRACTION80chain 'G' and (resid 140 through 211 )
81X-RAY DIFFRACTION81chain 'I' and (resid 1 through 119 )
82X-RAY DIFFRACTION82chain 'I' and (resid 120 through 145 )
83X-RAY DIFFRACTION83chain 'I' and (resid 146 through 223 )

+
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://pdbjlvh1.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