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- PDB-4jvp: Three dimensional structure of broadly neutralizing anti - Hepati... -

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Basic information

Entry
Database: PDB / ID: 4jvp
TitleThree dimensional structure of broadly neutralizing anti - Hepatitis C virus (HCV) glycoprotein E2 alpaca nanobody D03
ComponentsAnti-HCV E2 alpaca nanobody D03
KeywordsIMMUNE SYSTEM / Heavy-chain antibody / nanobody / Immunoglobulin fold / Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesVicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsKrey, T. / Rey, F.A.
CitationJournal: Hepatology / Year: 2013
Title: An alpaca nanobody inhibits hepatitis C virus entry and cell-to-cell transmission.
Authors: Tarr, A.W. / Lafaye, P. / Meredith, L. / Damier-Piolle, L. / Urbanowicz, R.A. / Meola, A. / Jestin, J.L. / Brown, R.J. / McKeating, J.A. / Rey, F.A. / Ball, J.K. / Krey, T.
History
DepositionMar 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-HCV E2 alpaca nanobody D03
B: Anti-HCV E2 alpaca nanobody D03
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,08712
Polymers31,1262
Non-polymers96110
Water2,378132
1
A: Anti-HCV E2 alpaca nanobody D03
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0446
Polymers15,5631
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Anti-HCV E2 alpaca nanobody D03
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0446
Polymers15,5631
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-120 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.806, 52.806, 182.471
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Antibody Anti-HCV E2 alpaca nanobody D03


Mass: 15563.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): K12
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2005mM LiSO4 , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2012
RadiationMonochromator: LN2 cooled Fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. all: 28387 / Num. obs: 26939 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 23.89 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 7.7
Reflection shellResolution: 1.76→1.86 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 1.6 / Num. unique all: 4095 / % possible all: 69.5

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
BUSTER2.9.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3STB
Resolution: 1.76→44.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.9578 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 1371 5.1 %RANDOM
Rwork0.1823 ---
obs0.1834 26863 94.61 %-
all-28367 --
Displacement parametersBiso mean: 35.55 Å2
Baniso -1Baniso -2Baniso -3
1--1.4926 Å20 Å20 Å2
2---1.4926 Å20 Å2
3---2.9851 Å2
Refine analyzeLuzzati coordinate error obs: 0.215 Å
Refinement stepCycle: LAST / Resolution: 1.76→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 0 50 132 2127
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012089HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.142848HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d701SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes47HARMONIC2
X-RAY DIFFRACTIONt_gen_planes320HARMONIC5
X-RAY DIFFRACTIONt_it2089HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.89
X-RAY DIFFRACTIONt_other_torsion18.02
X-RAY DIFFRACTIONt_chiral_improper_torsion263SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance3HARMONIC1
X-RAY DIFFRACTIONt_utility_angle6HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact2552SEMIHARMONIC4
LS refinement shellResolution: 1.76→1.83 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2271 84 3.91 %
Rwork0.2022 2063 -
all0.2032 2147 -
obs--94.61 %
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)
18.83-9.88250.58657.744-5.33410.49240.3061-0.0413-0.7557-0.3449-0.08710.80520.43890.1391-0.2190.1381-0.0694-0.0691-0.02320.0610.14778.5745-11.4779-7.6826
212.27234.2801-5.55732.4888-2.04050.66770.4522-0.6815-0.26630.1103-0.0537-0.33470.02910.406-0.39850.12190.0341-0.04250.26150.09050.072119.5139-4.45858.6513
31.9481-1.1808-0.49172.9169-1.8966.01320.3350.4523-0.9093-0.52230.11540.14910.5724-0.2397-0.45030.2140.0303-0.03270.2524-0.12490.099613.365-8.5305-12.2114
42.3049-1.51354.59851.02512.04464.21030.22510.38-0.2005-0.18450.2207-0.01990.25031.3837-0.44580.053-0.0217-0.02130.104-0.0087-0.04219.9443-1.8082-17.1415
52.7059-3.3212-6.08589.35051.12460-0.4354-0.3937-0.02440.6616-0.00010.0191-0.21120.28530.4355-0.02870.0222-0.02440.1018-0.008-0.07756.32434.23152.6708
67.8653-0.8044-3.435-2.2669-0.1825.5915-0.0202-0.31230.4144-0.206-0.00640.0557-0.44270.3520.0266-0.0455-0.0172-0.0215-0.0558-0.0257-0.02828.14145.902-3.9878
78.869-2.094-6.90880.62481.925812.9741-0.06331.2933-0.4551-0.2749-0.1377-0.47810.46340.98290.2010.0528-0.00140.03950.3515-0.0254-0.001215.97610.692-20.0475
88.296-1.97920.27674.4482-2.12319.6448-0.10870.48210.1368-0.02810.087-0.1986-0.47020.34980.0218-0.2173-0.0692-0.0287-0.15340.0321-0.218818.11626.1403-9.9207
95.609-1.26261.632410.64487.66330.6289-0.39140.70650.477-0.45960.1457-0.4179-0.08460.57250.2457-0.1971-0.03570.0036-0.0540.0665-0.20721.40272.1287-5.7741
102.92821.4702-7.67145.01582.07849.5042-0.05671.0703-1.0195-0.85770.0998-0.40630.94460.4453-0.04310.25010.1596-0.00630.2648-0.19180.020517.6443-11.0316-15.4439
114.36174.76817.814512.3076-1.861110.23750.3761-0.6615-0.18170.1569-0.37670.08640.2606-0.21090.0006-0.09020.00030.00050.0832-0.0246-0.061619.8356-3.7326-3.7956
1215.77594.1357-0.1094-0.4831-0.39272.85680.20280.32010.31650.1515-0.24-0.0522-0.31640.01180.0372-0.08920.00270.0303-0.0241-0.0114-0.109819.61252.5984.5307
133.48041.53272.13490.6097-0.39273.7705-0.0673-0.09980.0018-0.11380.01710.06370.1314-0.05850.0502-0.11780.00930.0046-0.04450.0142-0.13589.2631-1.7239-1.7593
146.69763.713-4.62439.1512-1.00021.9827-0.08330.37190.2144-0.45660.20120.06430.1416-0.0903-0.1179-0.0223-0.045-0.02180.04830.0472-0.08457.26832.7014-18.5914
1511.3751-5.6831.11348.0076-5.18144.9276-0.0884-0.52440.99720.36330.44760.4003-0.5154-0.3754-0.35920.0060.001-0.02080.01260.03020.09535.47858.5018-11.6038
165.31780.2757-0.8759-1.4394-1.76835.5494-0.1383-0.04540.37680.22480.08960.1467-0.48240.080.0486-0.1638-0.0449-0.0115-0.12580.0282-0.23521.39910.5597-11.8534
171.56340.02424.42451.28562.99317.96720.1438-0.4263-0.233-0.208-0.14170.0970.3854-0.2217-0.0021-0.1474-0.0265-0.0137-0.1080.0372-0.22359.0571-6.40451.0201
18-0.2616-0.3323-4.21256.2734-4.33958.5043-0.1576-0.3609-0.31150.6253-0.33110.02850.19380.92280.4887-0.17320.00950.0245-0.00340.1009-0.221117.4794-6.715514.6469
198.38014.41196.875812.8114-0.240910.59790.3142-0.14790.76110.4512-0.1524-0.334-0.1431.0937-0.1618-0.229-0.03450.0719-0.2374-0.0467-0.0921-5.650512.4968-14.39
202.92262.63522.63874.40642.70263.49950.397-0.32190.38360.06110.11720.3182-0.306-0.3256-0.5142-0.19330.0620.0612-0.0948-0.0881-0.2155-17.96866.37675.9078
218.98211.4122-3.85384.3892-4.03327.3030.50770.0280.67610.4188-0.11650.1607-0.5323-0.1763-0.3911-0.18920.02530.0206-0.08380.0078-0.2458-19.41937.356-2.1486
22-1.78411.955-6.79392.85210.18339.11210.2934-0.0887-0.4968-0.25970.1365-0.1523-0.59780.3035-0.4298-0.06620.05640.08340.02850.0604-0.0544-9.55939.2606-19.3751
233.09642.76531.10248.0862-5.43068.5416-0.04420.54580.1534-1.29110.2234-0.0115-0.034-1.1414-0.17920.098-0.03460.00450.02390.0136-0.1639-11.16631.9776-21.5288
2410.5399-2.1815-6.76073.39470.65738.55850.1763-0.18670.296-0.20740.06770.01450.2297-0.2528-0.244-0.1882-0.03010.0227-0.1458-0.0328-0.2012-9.3031-0.6182-4.5668
255.09070.03464.55181.77280.86372.83570.0019-0.4785-0.14460.1527-0.0014-0.0460.4369-0.6313-0.0005-0.1562-0.01630.0253-0.06930.0259-0.19-7.1852-6.0595-1.2472
2611.63931.84055.37475.4879-0.204414.2184-0.24641.14240.3561-0.30380.11050.4848-0.6256-0.140.1359-0.0798-0.0464-0.04860.10350.0294-0.1805-15.5218-0.768-19.7724
276.5208-2.1485-1.6956.29410.303816.5216-0.23160.3658-0.6111-0.1212-0.14610.48150.7021-0.60510.3777-0.3099-0.06510.0052-0.2049-0.0602-0.2346-19.0344-6.5308-9.9764
286.40860.6046-3.65796.6442-5.27341.9874-0.24250.378-0.3991-0.13520.14180.2933-0.0286-0.57470.1007-0.2719-0.0071-0.022-0.1527-0.027-0.3048-21.8595-1.0575-5.8561
290.92140.2037.96840.2484-2.139311.44130.1611.38380.9779-0.7378-0.22990.486-0.6459-0.20220.06890.09730.15450.02420.18970.2086-0.0548-18.662510.5787-15.643
30-3.8582.2274-5.94943.858-1.35655.96710.4839-0.2399-0.03140.0531-0.2110.2321-0.13530.2522-0.2729-0.1946-0.0093-0.00460.02430.024-0.1218-21.62461.9645-1.077
3115.1631.6707-5.6671-0.30450.49563.5471-0.0578-0.3525-0.66730.22710.09250.0150.17330.1573-0.0347-0.06180.0006-0.01180.05990.0174-0.084-14.1538-2.41954.5949
326.41420.4697-6.52613.71232.985413.30830.073-0.0042-0.0079-0.13080.1715-0.0694-0.4995-0.1366-0.2444-0.08590.00250.0019-0.0563-0.0334-0.1053-8.34852.9176-7.0057
335.0866-4.30795.02046.75332.20474.619-0.01860.40210.0672-0.80740.4092-0.1915-0.1456-0.0497-0.3906-0.054-0.09810.03510.0234-0.0824-0.1727-7.6364-3.931-18.6434
347.69842.91840.29299.977-3.270515.9646-0.09120.1991-0.4434-0.16650.0174-0.17970.54640.30850.0738-0.1306-0.01310.0277-0.1171-0.051-0.1021-8.0929-8.1596-10.9124
353.491-0.1853-3.4612-0.3644-3.22631.81650.1276-0.0715-0.41990.3117-0.1080.2539-0.08930.4115-0.0196-0.0209-0.0370.0110.0358-0.0156-0.1223-2.0106-4.7135-13.8586
366.14622.5748-2.25720.9244-7.81585.28460.3035-0.12890.1264-0.0859-0.256-0.0013-1.06540.1771-0.0476-0.1277-0.05660.0274-0.1449-0.0267-0.1876-3.85185.718-7.5329
37-3.07462.05765.5225.1831.17952.2442-0.1697-0.27060.06480.2246-0.20490.1655-0.1576-0.57250.3746-0.14210.0235-0.02930.0445-0.0601-0.1842-15.85586.188711.0929
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|5 - B|11 }B5 - 11
2X-RAY DIFFRACTION2{ B|12 - B|18 }B12 - 18
3X-RAY DIFFRACTION3{ B|19 - B|31 }B19 - 31
4X-RAY DIFFRACTION4{ B|32 - B|39 }B32 - 39
5X-RAY DIFFRACTION5{ B|40 - B|45 }B40 - 45
6X-RAY DIFFRACTION6{ B|46 - B|51 }B46 - 51
7X-RAY DIFFRACTION7{ B|52 - B|58 }B52 - 58
8X-RAY DIFFRACTION8{ B|59 - B|66 }B59 - 66
9X-RAY DIFFRACTION9{ B|67 - B|73 }B67 - 73
10X-RAY DIFFRACTION10{ B|74 - B|82 }B74 - 82
11X-RAY DIFFRACTION11{ B|83 - B|85 }B83 - 85
12X-RAY DIFFRACTION12{ B|86 - B|91 }B86 - 91
13X-RAY DIFFRACTION13{ B|92 - B|99 }B92 - 99
14X-RAY DIFFRACTION14{ B|100 - B|105 }B100 - 105
15X-RAY DIFFRACTION15{ B|106 - B|114 }B106 - 114
16X-RAY DIFFRACTION16{ B|115 - B|120 }B115 - 120
17X-RAY DIFFRACTION17{ B|121 - B|126 }B121 - 126
18X-RAY DIFFRACTION18{ B|127 - B|132 }B127 - 132
19X-RAY DIFFRACTION19{ A|3 - A|8 }A3 - 8
20X-RAY DIFFRACTION20{ A|9 - A|17 }A9 - 17
21X-RAY DIFFRACTION21{ A|18 - A|23 }A18 - 23
22X-RAY DIFFRACTION22{ A|24 - A|31 }A24 - 31
23X-RAY DIFFRACTION23{ A|32 - A|37 }A32 - 37
24X-RAY DIFFRACTION24{ A|38 - A|41 }A38 - 41
25X-RAY DIFFRACTION25{ A|42 - A|51 }A42 - 51
26X-RAY DIFFRACTION26{ A|52 - A|56 }A52 - 56
27X-RAY DIFFRACTION27{ A|58 - A|67 }A58 - 67
28X-RAY DIFFRACTION28{ A|68 - A|73 }A68 - 73
29X-RAY DIFFRACTION29{ A|74 - A|82 }A74 - 82
30X-RAY DIFFRACTION30{ A|83 - A|88 }A83 - 88
31X-RAY DIFFRACTION31{ A|89 - A|95 }A89 - 95
32X-RAY DIFFRACTION32{ A|96 - A|100 }A96 - 100
33X-RAY DIFFRACTION33{ A|101 - A|106 }A101 - 106
34X-RAY DIFFRACTION34{ A|107 - A|111 }A107 - 111
35X-RAY DIFFRACTION35{ A|112 - A|117 }A112 - 117
36X-RAY DIFFRACTION36{ A|118 - A|123 }A118 - 123
37X-RAY DIFFRACTION37{ A|124 - A|132 }A124 - 132

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