[English] 日本語
Yorodumi
- PDB-6ewb: Crystal structure of GII.4 UNSW 2012 P domain in complex with Fab 10E9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ewb
TitleCrystal structure of GII.4 UNSW 2012 P domain in complex with Fab 10E9
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
  • VP1
KeywordsVIRAL PROTEIN / protein-Fab complex / Fab fragment of IgG / norovirus / antibody
Function / homology
Function and homology information


Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesNorovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.78 Å
AuthorsKoromyslova, A.D. / Hansman, G.S.
Citation
Journal: J.Virol. / Year: 2019
Title: Human Norovirus Neutralized by a Monoclonal Antibody Targeting the Histo-Blood Group Antigen Pocket.
Authors: Koromyslova, A.D. / Morozov, V.A. / Hefele, L. / Hansman, G.S.
#1: Journal: Biorxiv / Year: 2019
Title: Human Norovirus Neutralized by a Monoclonal Antibody Targeting the HBGA 1 Pocket
Authors: Koromyslova, A.D. / Morozov, V.M. / Hefele, L. / Hansman, G.S.
History
DepositionNov 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _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: VP1
B: VP1
C: VP1
D: VP1
E: Fab heavy chain
F: Fab light chain
G: Fab heavy chain
H: Fab heavy chain
I: Fab light chain
J: Fab heavy chain
K: Fab light chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,88014
Polymers323,75612
Non-polymers1242
Water0
1
A: VP1
B: VP1
E: Fab heavy chain
F: Fab light chain
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,0028
Polymers161,8786
Non-polymers1242
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: VP1
D: VP1
G: Fab heavy chain
I: Fab light chain
J: Fab heavy chain
K: Fab light chain


Theoretical massNumber of molelcules
Total (without water)161,8786
Polymers161,8786
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.838, 111.626, 288.255
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
12chain E
22chain G
32chain H
42chain J
13chain F
23chain I
33chain K
43chain L

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERMETMETchain AAA224 - 5304 - 310
21LYSLYSMETMETchain BBB225 - 5305 - 310
31GLYGLYMETMETchain CCC221 - 5301 - 310
41PROPROMETMETchain DDD222 - 5302 - 310
12GLNGLNVALVALchain EEE1 - 2141 - 214
22GLNGLNARGARGchain GGG1 - 2161 - 216
32GLNGLNARGARGchain HHH1 - 2161 - 216
42GLNGLNPROPROchain JJJ1 - 2151 - 215
13GLNGLNASNASNchain FFF1 - 2092 - 210
23GLYGLYARGARGchain III0 - 2101 - 211
33GLYGLYARGARGchain KKK0 - 2101 - 211
43GLNGLNARGARGchain LLL1 - 2102 - 211

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein
VP1


Mass: 34272.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Plasmid: pMBP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: K4LM89
#2: Antibody
Fab heavy chain / Fragment antigen-binding


Mass: 23131.838 Da / Num. of mol.: 4 / Fragment: VHH
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody
Fab light chain / Fragment antigen-binding


Mass: 23534.939 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M calcium acetate, 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 29, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.78→48.757 Å / Num. obs: 86711 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 13.88 % / Biso Wilson estimate: 55.92 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.156 / Χ2: 1.086 / Net I/σ(I): 17.97
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.78-2.9513.5840.942.71130210.840.97592.9
2.95-3.1514.6110.5894.82131310.9440.61100
3.15-3.414.4770.3678.01122650.9770.381100
3.4-3.7214.3060.21913.49113410.9920.227100
3.72-4.1613.9640.13620.86102700.9960.14199.9
4.16-4.812.8610.08530.8991210.9980.08899.9
4.8-5.8612.8530.07234.2177920.9980.075100
5.86-8.2314.2680.06339.8961300.9990.065100
8.23-48.75712.8310.04355.2936400.9990.04599.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.95 Å48.76 Å
Translation8.95 Å48.76 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J4W, 4X0C
Resolution: 2.78→48.757 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.35
RfactorNum. reflection% reflection
Rfree0.2219 4335 5 %
Rwork0.1859 --
obs0.1877 86655 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 184.05 Å2 / Biso mean: 59.1046 Å2 / Biso min: 18.07 Å2
Refinement stepCycle: final / Resolution: 2.78→48.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21701 0 8 0 21709
Biso mean--65.54 --
Num. residues----2890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00522311
X-RAY DIFFRACTIONf_angle_d0.95530522
X-RAY DIFFRACTIONf_chiral_restr0.0363461
X-RAY DIFFRACTIONf_plane_restr0.0053940
X-RAY DIFFRACTIONf_dihedral_angle_d11.5057687
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5752X-RAY DIFFRACTION8.76TORSIONAL
12B5752X-RAY DIFFRACTION8.76TORSIONAL
13C5752X-RAY DIFFRACTION8.76TORSIONAL
14D5752X-RAY DIFFRACTION8.76TORSIONAL
21E3488X-RAY DIFFRACTION8.76TORSIONAL
22G3488X-RAY DIFFRACTION8.76TORSIONAL
23H3488X-RAY DIFFRACTION8.76TORSIONAL
24J3488X-RAY DIFFRACTION8.76TORSIONAL
31F3641X-RAY DIFFRACTION8.76TORSIONAL
32I3641X-RAY DIFFRACTION8.76TORSIONAL
33K3641X-RAY DIFFRACTION8.76TORSIONAL
34L3641X-RAY DIFFRACTION8.76TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7785-2.81010.4374970.35941834193166
2.8101-2.84320.3591420.266527062848100
2.8432-2.87780.29621460.261927642910100
2.8778-2.91430.27441440.262927382882100
2.9143-2.95260.31851440.250727462890100
2.9526-2.9930.27071430.249827112854100
2.993-3.03580.24471450.238927532898100
3.0358-3.08110.26581450.238427552900100
3.0811-3.12920.26491440.228527332877100
3.1292-3.18050.28321440.232927442888100
3.1805-3.23540.27751470.238327792926100
3.2354-3.29420.28751440.22827392883100
3.2942-3.35750.26681450.219427582903100
3.3575-3.4260.24121450.211127512896100
3.426-3.50050.24541440.202727412885100
3.5005-3.58190.23771460.19727702916100
3.5819-3.67150.20451450.190827512896100
3.6715-3.77070.21961460.181327662912100
3.7707-3.88160.22811450.182527622907100
3.8816-4.00680.19751450.173727572902100
4.0068-4.150.19611460.164527802926100
4.15-4.3160.18531460.149127832929100
4.316-4.51230.17361450.138727562901100
4.5123-4.75010.14931480.135927992947100
4.7501-5.04740.17941470.141328052952100
5.0474-5.43660.18591480.148728052953100
5.4366-5.98290.24551490.166728222971100
5.9829-6.84660.19911490.179428282977100
6.8466-8.61820.19461520.168428833035100
8.6182-48.76410.22361590.190130013160100
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)
10.7373-0.6205-1.16182.67181.96792.0485-0.21340.083-0.06690.09670.10830.13890.12440.19610.09570.2216-0.004-0.01020.382-0.05630.3499-24.5559-5.3032-72.99
24.3517-0.396-1.05331.08371.14383.33580.1077-0.03320.0193-0.07310.04320.0812-0.1794-0.0743-0.19070.2514-0.0238-0.01430.2339-0.05520.253-31.39296.9743-66.5344
30.7501-0.4971-0.50391.34140.32070.9473-0.05290.0231-0.065-0.19720.1124-0.26120.05360.2059-0.06540.2243-0.02590.02460.4068-0.0980.3239-18.4209-10.2592-84.1183
41.4919-0.13070.26852.9195-1.47661.7403-0.01810.4022-0.2043-0.3044-0.05480.16360.1462-0.06520.07220.23390.0049-0.01880.4067-0.15860.4097-43.585-10.8058-78.5987
51.5268-0.5296-0.10222.073-0.1721.751-0.03330.1601-0.42690.00540.01270.40110.2031-0.1111-0.01950.1969-0.0444-0.00140.2691-0.06810.3851-44.9074-17.0212-67.7008
60.962-0.53370.36953.8454-0.60591.8675-0.01550.02880.05580.1241-0.061-0.4091-0.14090.23570.08510.1498-0.00530.00410.3658-0.02810.2314-14.302712.4957-21.2932
71.38780.4196-0.36482.3352-0.49541.9815-0.0908-0.1119-0.29570.0087-0.0819-0.33190.25920.25080.20990.22840.0769-0.0230.36380.0040.2615-11.18770.7705-22.9766
81.57720.6756-0.88231.1962-0.10552.0449-0.06210.2369-0.0036-0.06130.0215-0.0162-0.0242-0.03580.08220.17720.026-0.03710.24060.00480.2052-33.931910.0165-26.811
97.14591.5522-0.57831.71410.81571.6454-0.13960.5256-0.4343-0.11960.1654-0.3940.04170.005-0.02450.25320.0025-0.02380.34850.00630.1865-27.64949.987-42.5769
100.58430.1452-0.59371.4287-0.30221.64410.04530.05890.02480.15120.11920.1742-0.0877-0.2486-0.19360.19920.02040.01090.28590.0270.2102-39.762714.1452-18.5332
111.794-0.37490.90442.7711-1.35183.19940.03210.42080.5675-0.20370.06630.1702-0.6425-0.3416-0.04710.65570.0460.16210.50520.11210.6104-28.119826.3388-103.8657
123.78921.26290.38566.53660.41143.43830.33940.18740.3760.7898-0.40840.8291-0.3042-0.8013-0.1140.85270.04280.15970.83370.14110.7037-21.258626.4532-136.2221
135.08091.35591.10282.0244-1.87584.88010.52880.78460.1696-0.8319-0.162-0.70040.05750.2125-0.22460.57080.030.09830.75080.04460.5004-9.62887.8661-110.2901
143.5137-0.1588-0.70313.56911.68870.9240.4947-0.389-0.08570.10480.1828-0.4078-0.52250.0232-0.60490.6468-0.07330.1620.63820.06940.5161-14.10627.7951-101.6816
156.69010.5043-1.02736.5042-0.34894.95390.28420.1137-0.3288-0.8149-0.30550.3826-0.6331-0.15370.08290.540.02340.02740.4207-0.04920.2913-23.88384.5045-106.4874
165.3522-1.65510.96786.2935-1.73484.1963-0.20910.34950.3491-0.74270.2036-0.13710.15390.0242-0.0010.5144-0.02860.14630.44970.01850.3487-15.98666.7971-105.0383
170.6191-0.3978-0.85540.8931.6423.0381-0.3020.1946-0.0325-0.8999-0.5583-0.15150.89080.21030.56691.41050.15320.33430.79840.14650.4786-10.57085.3616-126.0469
185.25561.51290.67611.53560.58894.8399-0.55030.58390.8309-0.5121-0.5658-0.19750.46690.57831.07790.9952-0.02610.07551.12840.47990.9504-11.514529.9536-143.451
193.5965-1.82461.78058.4023-0.73252.5025-0.23670.40220.3271-0.42290.0738-0.00170.00570.1286-0.03241.1515-0.02790.16910.88390.3110.6858-8.675517.2094-134.5185
201.5283-1.5841-1.35513.6686-0.73464.3587-0.18120.49140.30470.02010.139-0.15980.2876-0.03160.01450.7198-0.14230.09240.96460.23660.7439-6.347519.5831-132.097
210.73620.78720.40821.68591.05670.69620.08480.50910.5481-0.0965-0.3218-0.7638-0.70160.36460.2011.2361-0.52560.11121.32030.56870.9221-4.958232.669-138.7496
221.4305-2.01451.32787.4814-2.38382.8466-0.46870.46520.08620.31770.2201-0.1645-0.33780.94530.26240.97080.00230.3850.94920.37961.24730.395719.1803-141.0087
238.4485-1.2068-3.0051.49670.80512.6352-0.09320.0481-0.6724-0.0719-0.18240.198-0.1009-0.10310.32960.25980.00810.0150.318-0.05430.34134.490811.6229-62.4316
242.66561.4062-1.32312.25690.97354.16880.0169-0.4145-0.1325-0.02780.0068-0.19730.07540.3486-0.0420.16710.02410.01660.28010.01070.305110.942111.576-54.7592
251.0907-0.6577-1.27651.81.95542.5410.01720.1363-0.3447-0.22280.017-0.0698-0.1822-0.1168-0.08680.21390.03330.00630.3411-0.05840.470511.962-4.2125-70.2467
261.94562.75820.74495.55560.771.7117-0.12030.1825-0.181-0.2988-0.12420.71550.0332-0.34650.1790.29930.02570.1080.4078-0.15380.784812.2281-12.5089-82.0824
273.607-2.2841-1.291.75970.78542.5114-0.10330.1079-0.05030.0309-0.010.1105-0.1301-0.14350.09290.2077-0.0209-0.05660.21110.00780.2421-67.496813.8257-52.4976
283.9931-1.04240.60763.88130.23085.55930.1457-0.02490.158-0.3567-0.1452-0.4026-0.6581-0.2047-0.0820.42070.1217-0.00960.42460.04050.362-72.134117.1748-19.9909
292.1526-0.62240.08063.2459-0.25071.3804-0.5173-0.8652-1.22190.22420.13790.04790.43010.13840.35230.42530.12830.26810.48850.16890.73973.5472-9.9339-44.9336
300.9246-1.1002-1.31871.55872.04962.8073-0.2724-0.0517-0.50920.3518-0.02450.13820.4580.10940.41520.37620.08690.17360.38850.06980.882311.1371-14.162-60.5853
315.67620.0291-2.93132.0252-0.67434.95370.138-0.2086-0.2870.29650.17080.2162-0.02460.3743-0.32370.46370.03160.12040.393-0.15520.950624.4397-23.203-73.8749
322.5592-0.37940.2715.0414-0.00741.4942-0.15810.31990.3213-0.62720.0258-0.4922-0.39670.120.09960.54760.08670.09960.30850.0730.3934-34.316150.4336-39.1788
330.7484-0.7342-1.03913.70281.22871.08010.42290.08460.1791-0.0998-0.24170.0523-0.5831-0.0218-0.12290.68680.09390.1010.38880.03830.4019-42.863164.3935-29.1592
344.56741.32512.76035.28741.2588.69870.5750.08020.38480.0499-0.1668-0.4047-0.37441.6681-0.29310.9978-0.05630.22130.6971-0.02830.5427-43.865977.7863-18.8593
353.32911.02312.54433.83571.55932.7199-0.1165-0.19020.31520.3398-0.20660.3409-0.4035-0.66260.23930.45890.1273-0.00060.3180.00780.3275-53.095843.0459-17.8011
362.9947-0.0803-0.20661.0776-0.52152.4883-0.0392-0.1113-0.13550.1993-0.0398-0.1899-0.2999-0.07450.07080.46830.10240.00350.26190.03070.2794-42.939938.8224-19.8214
374.0358-1.0272-0.56386.17743.09146.15110.34450.01970.17250.55860.318-0.2346-0.24040.2141-0.66510.4670.06420.0160.3619-0.04590.3755-44.743746.2389-13.9781
380.99710.1871-0.75481.0538-0.65180.55260.2690.23360.60080.28980.07180.3818-0.5789-0.0321-0.29650.89190.1790.19080.34030.10410.6536-54.725664.9546-17.463
393.4844-0.99580.48154.7644-1.99214.56330.46010.47010.9654-0.6731-0.5163-0.31910.3804-0.13870.01980.6630.0890.07380.43940.06780.5066-56.014369.3375-16.706
400.2494-0.5401-0.07091.61150.188-0.00540.63980.59740.1969-0.2410.20791.0222-0.5994-0.6127-0.66831.02610.73610.3490.14130.9091.634-66.24578.1458-12.439
412.38160.9981-0.53582.82481.52251.424-0.133-0.1604-0.05590.6631-0.07140.2074-0.04780.39270.09540.4042-0.01640.04550.38570.08680.5019-65.8097-10.5809-40.5101
423.81950.64090.57693.58690.06473.1002-0.11960.1431-0.53330.21420.0391-0.0440.18070.1480.06830.2256-0.00570.06250.24610.03350.3934-57.8887-7.2608-47.2938
431.794-1.92792.79793.0123-1.78178.9854-0.26910.49440.1140.2696-0.04660.0759-0.23490.73870.25690.2982-0.0380.14170.27180.10560.4364-58.2335-5.5442-38.1057
442.0314-0.5055-1.80368.26824.82617.0138-0.25050.09280.3655-0.7195-0.72160.4760.0467-0.36560.90760.28590.007-0.09380.29720.06450.3522-66.1792-2.8799-55.879
451.827-2.3158-2.70893.07533.45013.9587-0.4242-0.34450.16270.82790.4059-0.04161.0514-0.37870.03390.52760.04030.01210.51650.20340.5113-64.686-6.9636-25.1038
467.6642-3.0319-2.63646.82693.22384.2711-0.3009-0.1501-0.20090.4284-0.07910.61550.1588-0.71860.46410.4470.08450.09970.61370.0790.3774-79.02086.7643-15.3647
475.1278-3.0341-2.33743.87270.74057.63860.07230.3842-0.17070.1764-0.2376-0.15240.2854-0.78070.24860.5501-0.11590.01310.58540.08580.5077-76.00581.5566-21.3867
485.8004-1.8883-3.58070.60731.16692.224-0.6745-0.0783-0.43060.53130.33820.8755-0.0942-1.38780.36230.64260.28370.16031.31860.11110.5487-88.173711.0111-15.178
494.2948-2.1809-0.2092.62232.09493.3803-0.8579-0.8509-0.43630.36720.52360.07480.6937-0.55650.38140.79280.10140.36420.8720.20410.7382-81.73230.1487-8.7442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 224 through 313 )A224 - 313
2X-RAY DIFFRACTION2chain 'A' and (resid 314 through 380 )A314 - 380
3X-RAY DIFFRACTION3chain 'A' and (resid 381 through 530 )A381 - 530
4X-RAY DIFFRACTION4chain 'B' and (resid 225 through 352 )B225 - 352
5X-RAY DIFFRACTION5chain 'B' and (resid 353 through 530 )B353 - 530
6X-RAY DIFFRACTION6chain 'C' and (resid 221 through 352 )C221 - 352
7X-RAY DIFFRACTION7chain 'C' and (resid 353 through 530 )C353 - 530
8X-RAY DIFFRACTION8chain 'D' and (resid 222 through 303 )D222 - 303
9X-RAY DIFFRACTION9chain 'D' and (resid 304 through 379 )D304 - 379
10X-RAY DIFFRACTION10chain 'D' and (resid 380 through 530 )D380 - 530
11X-RAY DIFFRACTION11chain 'E' and (resid 1 through 122 )E1 - 122
12X-RAY DIFFRACTION12chain 'E' and (resid 123 through 214 )E123 - 214
13X-RAY DIFFRACTION13chain 'F' and (resid 1 through 18 )F1 - 18
14X-RAY DIFFRACTION14chain 'F' and (resid 19 through 37 )F19 - 37
15X-RAY DIFFRACTION15chain 'F' and (resid 38 through 60 )F38 - 60
16X-RAY DIFFRACTION16chain 'F' and (resid 61 through 100 )F61 - 100
17X-RAY DIFFRACTION17chain 'F' and (resid 101 through 112 )F101 - 112
18X-RAY DIFFRACTION18chain 'F' and (resid 113 through 127 )F113 - 127
19X-RAY DIFFRACTION19chain 'F' and (resid 128 through 143 )F128 - 143
20X-RAY DIFFRACTION20chain 'F' and (resid 144 through 173 )F144 - 173
21X-RAY DIFFRACTION21chain 'F' and (resid 174 through 187 )F174 - 187
22X-RAY DIFFRACTION22chain 'F' and (resid 188 through 209 )F188 - 209
23X-RAY DIFFRACTION23chain 'G' and (resid 1 through 32 )G1 - 32
24X-RAY DIFFRACTION24chain 'G' and (resid 33 through 91 )G33 - 91
25X-RAY DIFFRACTION25chain 'G' and (resid 92 through 148 )G92 - 148
26X-RAY DIFFRACTION26chain 'G' and (resid 149 through 216 )G149 - 216
27X-RAY DIFFRACTION27chain 'H' and (resid 1 through 122 )H1 - 122
28X-RAY DIFFRACTION28chain 'H' and (resid 123 through 216 )H123 - 216
29X-RAY DIFFRACTION29chain 'I' and (resid 0 through 74 )I0 - 74
30X-RAY DIFFRACTION30chain 'I' and (resid 75 through 127 )I75 - 127
31X-RAY DIFFRACTION31chain 'I' and (resid 128 through 210 )I128 - 210
32X-RAY DIFFRACTION32chain 'J' and (resid 1 through 83 )J1 - 83
33X-RAY DIFFRACTION33chain 'J' and (resid 84 through 148 )J84 - 148
34X-RAY DIFFRACTION34chain 'J' and (resid 149 through 215 )J149 - 215
35X-RAY DIFFRACTION35chain 'K' and (resid 0 through 25 )K0 - 25
36X-RAY DIFFRACTION36chain 'K' and (resid 26 through 74 )K26 - 74
37X-RAY DIFFRACTION37chain 'K' and (resid 75 through 88 )K75 - 88
38X-RAY DIFFRACTION38chain 'K' and (resid 89 through 148 )K89 - 148
39X-RAY DIFFRACTION39chain 'K' and (resid 149 through 181 )K149 - 181
40X-RAY DIFFRACTION40chain 'K' and (resid 182 through 210 )K182 - 210
41X-RAY DIFFRACTION41chain 'L' and (resid 1 through 18 )L1 - 18
42X-RAY DIFFRACTION42chain 'L' and (resid 19 through 74 )L19 - 74
43X-RAY DIFFRACTION43chain 'L' and (resid 75 through 88 )L75 - 88
44X-RAY DIFFRACTION44chain 'L' and (resid 89 through 100 )L89 - 100
45X-RAY DIFFRACTION45chain 'L' and (resid 101 through 112 )L101 - 112
46X-RAY DIFFRACTION46chain 'L' and (resid 113 through 149 )L113 - 149
47X-RAY DIFFRACTION47chain 'L' and (resid 150 through 173 )L150 - 173
48X-RAY DIFFRACTION48chain 'L' and (resid 174 through 187 )L174 - 187
49X-RAY DIFFRACTION49chain 'L' and (resid 188 through 210 )L188 - 210

+
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