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- PDB-6j5f: Complex structure of MAb 4.2-scFv with tick-borne encephalitis vi... -

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Basic information

Entry
Database: PDB / ID: 6j5f
TitleComplex structure of MAb 4.2-scFv with tick-borne encephalitis virus envelope protein Domain III
Components
  • Envelope protein
  • antibody heavy chain
  • antibody light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / protective and neutralizing antibody / flavivirus envelope protein / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane => GO:0016020 / host cell endoplasmic reticulum membrane / protein dimerization activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane
Similarity search - Function
Immunoglobulin-like - #350 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain ...Immunoglobulin-like - #350 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesTick-borne encephalitis virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsYang, X. / Qi, J. / Peng, R. / Dai, L. / Gould, E.A. / Tien, P. / Gao, G.F.
CitationJournal: J. Virol. / Year: 2019
Title: Molecular Basis of a Protective/Neutralizing Monoclonal Antibody Targeting Envelope Proteins of both Tick-Borne Encephalitis Virus and Louping Ill Virus.
Authors: Yang, X. / Qi, J. / Peng, R. / Dai, L. / Gould, E.A. / Gao, G.F. / Tien, P.
History
DepositionJan 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope protein
H: antibody heavy chain
L: antibody light chain


Theoretical massNumber of molelcules
Total (without water)36,1793
Polymers36,1793
Non-polymers00
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-16 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.668, 95.461, 99.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-577-

HOH

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Components

#1: Protein Envelope protein


Mass: 11032.542 Da / Num. of mol.: 1 / Fragment: Domain III
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tick-borne encephalitis virus
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A096YGU7
#2: Antibody antibody heavy chain


Mass: 13169.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Antibody antibody light chain


Mass: 11977.288 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1% w/v tryptone, 0.05M HEPES sodium pH 7.0, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 41293 / % possible obs: 99.9 % / Redundancy: 12.7 % / Biso Wilson estimate: 24.68 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.103 / Net I/σ(I): 27.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 9.4 / Num. unique obs: 4076 / CC1/2: 0.807 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVB, 5GRJ
Resolution: 1.801→39.954 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.97
RfactorNum. reflection% reflection
Rfree0.1924 1949 5.01 %
Rwork0.1794 --
obs0.18 38897 94.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.801→39.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 0 354 2838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012551
X-RAY DIFFRACTIONf_angle_d0.8713468
X-RAY DIFFRACTIONf_dihedral_angle_d16.849916
X-RAY DIFFRACTIONf_chiral_restr0.077373
X-RAY DIFFRACTIONf_plane_restr0.004443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8006-1.84570.27321330.23121930X-RAY DIFFRACTION70
1.8457-1.89560.23981390.22842118X-RAY DIFFRACTION78
1.8956-1.95130.24231450.21642270X-RAY DIFFRACTION84
1.9513-2.01430.20031470.20292494X-RAY DIFFRACTION90
2.0143-2.08630.24571500.19552706X-RAY DIFFRACTION97
2.0863-2.16980.20991230.19212749X-RAY DIFFRACTION99
2.1698-2.26860.21961590.1942771X-RAY DIFFRACTION100
2.2686-2.38820.20661480.19422809X-RAY DIFFRACTION100
2.3882-2.53780.20311640.19752751X-RAY DIFFRACTION100
2.5378-2.73370.21251180.19152832X-RAY DIFFRACTION100
2.7337-3.00870.19231110.18712843X-RAY DIFFRACTION100
3.0087-3.44380.19911390.16962848X-RAY DIFFRACTION100
3.4438-4.3380.16611040.15362887X-RAY DIFFRACTION100
4.338-39.96430.13861690.15482940X-RAY DIFFRACTION99
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)
10.69280.242-0.14571.06720.42590.743-0.03580.05580.01770.00140.0467-0.2227-0.10870.23380.05940.0707-0.0485-0.00910.1869-0.00370.121333.947712.400645.6552
20.3961-0.1281-0.40380.5441-0.17020.58810.0378-0.08880.01780.36510.1637-0.2905-0.32410.57040.08920.1864-0.1009-0.04370.19820.00260.179930.612822.317441.5873
30.3843-0.4591-0.02370.5767-0.01310.0489-0.0501-0.0935-0.1770.14190.0030.52970.0219-0.2924-0.00350.1716-0.0269-0.01360.1394-0.01130.208225.39611.237858.488
40.7001-0.00530.4771.76880.03940.2986-0.02540.15050.07830.3897-0.0043-0.356-0.2730.33720.07480.1545-0.0823-0.05670.25290.00680.168834.791114.091550.8981
50.19510.0558-0.20130.18640.13710.3808-0.059-0.06570.07660.2252-0.0502-0.34290.13160.0019-0.00670.16910.0015-0.06960.1611-0.00180.140330.81513.778954.0064
60.02960.0196-0.00880.09890.06820.0609-0.05020.2684-0.0247-0.1632-0.00290.5012-0.0899-0.4371-0.0020.17670.00770.04430.18260.03920.234111.31431.439823.4063
70.03790.0436-0.00670.04730.01160.04-0.03130.20040.042-0.25270.0283-0.152-0.21330.206200.2688-0.03730.05510.21070.02020.154523.378725.01715.1132
80.3236-0.227-0.05170.1596-0.09280.4113-0.04190.09510.19670.02930.14530.0657-0.2617-0.14360.00570.2764-0.02680.04450.1392-0.00190.195119.061731.895422.1359
90.2384-0.17880.14520.1787-0.13150.0945-0.0470.00160.0552-0.00110.04030.038-0.197-0.0251-0.00210.1663-0.05450.02080.11750.01080.121519.717724.96626.1894
100.33040.068-0.24190.3294-0.37130.4864-0.03260.0487-0.0796-0.0996-0.017-0.12990.03230.0701-0.05130.1489-0.05520.00770.12790.01660.1223.562818.966123.8531
110.18670.1423-0.0250.1087-0.02890.06140.1572-0.1005-0.3979-0.0915-0.3139-0.66620.49970.47530.00190.2160.00920.02720.19850.0330.250730.441214.103318.8998
120.6254-0.04950.34990.1376-0.12360.25940.05910.04750.1652-0.0954-0.034-0.235-0.30810.1645-0.03930.2281-0.07330.03560.12970.00890.173126.115630.641721.3008
130.41840.1685-0.01130.6001-0.54560.5230.00290.07630.0343-0.02380.0378-0.08520.2147-0.040.01220.1697-0.04080.02030.12310.00150.117620.96519.866516.0624
140.05520.07530.01360.1338-0.14730.2321-0.0335-0.12710.21560.1520.00380.0773-0.3189-0.1083-0.00310.1527-0.0333-0.00070.13770.00680.142514.975622.437430.0484
150.0091-0.0419-0.03620.42630.34720.2888-0.22590.3215-0.0678-0.1448-0.0060.06470.25330.0177-0.08970.2545-0.07330.04620.19040.01140.09319.863521.13415.086
161.2491-0.0282-0.24940.1091-0.34621.28610.14080.093-0.3434-0.21790.1211-0.4044-0.230.02740.26240.1216-0.03980.050.1038-0.0510.218616.9383.185527.1116
170.0322-0.0213-0.02550.142-0.05610.0420.01030.0018-0.09-0.15990.04140.2846-0.09970.1086-00.1244-0.0103-0.02740.14930.00940.2328-4.28834.172522.6037
180.15760.0193-0.13080.1294-0.0160.10030.079-0.1691-0.27870.1148-0.02440.0260.0128-0.0342-00.1087-0.0249-0.00740.13880.01660.168112.74664.608334.0071
190.00870.03430.02350.10260.06810.0557-0.00190.12510.0957-0.08070.03380.0908-0.1564-0.00290.00040.0913-0.0339-0.01440.16070.02440.12568.443413.214427.3929
200.5203-0.10090.2030.0730.04590.249-0.07580.19080.2973-0.23850.0990.1797-0.2317-0.15830.04250.1904-0.0338-0.04260.17370.06650.19065.678418.36522.3519
210.38510.255-0.20120.2576-0.02890.24670.0634-0.42450.11780.2497-0.09680.2492-0.2311-0.1681-0.00290.1225-0.01670.02870.1768-0.01790.19373.272716.405635.9341
220.25840.0981-0.26230.1656-0.08410.25070.06-0.3755-0.28010.12520.02130.05760.0648-0.097600.1021-0.0204-0.00910.15180.02770.18485.54615.841634.6976
230.22120.0870.2920.0380.12010.4006-0.2474-0.10770.5149-0.0427-0.0274-0.0566-0.546-0.2247-0.02090.22020.0203-0.02340.20930.04510.3598-6.219412.52224.752
240.27680.3258-0.03230.3513-0.19070.2749-0.0810.0788-0.0798-0.06370.0918-0.0092-0.06560.060.01630.0868-0.0252-0.00160.12590.00170.098816.786910.978228.4356
250.0411-0.0344-0.11930.5110.64140.9885-0.01240.0506-0.2741-0.33940.31170.6311-0.0291-0.23940.11370.1909-0.0692-0.04610.22730.06780.3225-1.48886.226117.7846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 304 through 332 )
2X-RAY DIFFRACTION2chain 'A' and (resid 333 through 341 )
3X-RAY DIFFRACTION3chain 'A' and (resid 342 through 356 )
4X-RAY DIFFRACTION4chain 'A' and (resid 357 through 385 )
5X-RAY DIFFRACTION5chain 'A' and (resid 386 through 397 )
6X-RAY DIFFRACTION6chain 'H' and (resid 1 through 6 )
7X-RAY DIFFRACTION7chain 'H' and (resid 7 through 17 )
8X-RAY DIFFRACTION8chain 'H' and (resid 18 through 28 )
9X-RAY DIFFRACTION9chain 'H' and (resid 29 through 39 )
10X-RAY DIFFRACTION10chain 'H' and (resid 40 through 60 )
11X-RAY DIFFRACTION11chain 'H' and (resid 61 through 67 )
12X-RAY DIFFRACTION12chain 'H' and (resid 68 through 83 )
13X-RAY DIFFRACTION13chain 'H' and (resid 84 through 100 )
14X-RAY DIFFRACTION14chain 'H' and (resid 101 through 113 )
15X-RAY DIFFRACTION15chain 'H' and (resid 114 through 120 )
16X-RAY DIFFRACTION16chain 'L' and (resid 1 through 7 )
17X-RAY DIFFRACTION17chain 'L' and (resid 8 through 18 )
18X-RAY DIFFRACTION18chain 'L' and (resid 19 through 32 )
19X-RAY DIFFRACTION19chain 'L' and (resid 33 through 38 )
20X-RAY DIFFRACTION20chain 'L' and (resid 39 through 48 )
21X-RAY DIFFRACTION21chain 'L' and (resid 49 through 61 )
22X-RAY DIFFRACTION22chain 'L' and (resid 62 through 75 )
23X-RAY DIFFRACTION23chain 'L' and (resid 76 through 83 )
24X-RAY DIFFRACTION24chain 'L' and (resid 84 through 102 )
25X-RAY DIFFRACTION25chain 'L' and (resid 103 through 108 )

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