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- PDB-6mwn: Crystal structure of hepatitis A virus IRES domain V in complex w... -

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Basic information

Entry
Database: PDB / ID: 6mwn
TitleCrystal structure of hepatitis A virus IRES domain V in complex with Fab HAVx
Components
  • Fab HAVx Heavy Chain
  • Fab HAVx Light Chain
  • HAV dV RNA (92-MER)
KeywordsRNA/Immune System / RNA / Chaperone Assisted RNA Crystallography / Phage Display / Hepatitis A Virus / IRES / Fab Antibody / RNA-Immune System Complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
Hepatovirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.838 Å
AuthorsKoirala, D. / Shao, Y. / Piccirilli, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01AI081987 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM102489 United States
CitationJournal: Nat Commun / Year: 2019
Title: A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites.
Authors: Koirala, D. / Shao, Y. / Koldobskaya, Y. / Fuller, J.R. / Watkins, A.M. / Shelke, S.A. / Pilipenko, E.V. / Das, R. / Rice, P.A. / Piccirilli, J.A.
History
DepositionOct 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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: HAV dV RNA (92-MER)
B: HAV dV RNA (92-MER)
C: Fab HAVx Heavy Chain
D: Fab HAVx Light Chain
H: Fab HAVx Heavy Chain
L: Fab HAVx Light Chain


Theoretical massNumber of molelcules
Total (without water)167,3806
Polymers167,3806
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, gel filtration, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15680 Å2
ΔGint-119 kcal/mol
Surface area66420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.149, 100.582, 236.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: RNA chain HAV dV RNA (92-MER)


Mass: 29750.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Hepatitis A Virus IRES Domain V / Source: (synth.) Hepatovirus A / References: GenBank: 329582
#2: Antibody Fab HAVx Heavy Chain


Mass: 27588.012 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Antibody fragment (Fab) that binds to domain V of Hepatitis A Virus IRES
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Fab HAVx Light Chain


Mass: 26351.588 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033202 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 10, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033202 Å / Relative weight: 1
ReflectionResolution: 2.838→29.607 Å / Num. obs: 42565 / % possible obs: 99.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 74.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1004 / Rpim(I) all: 0.04158 / Rrim(I) all: 0.1088 / Net I/av σ(I): 13.89 / Net I/σ(I): 13.89
Reflection shellResolution: 2.838→2.94 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.38 / Num. unique obs: 4057 / CC1/2: 0.595 / Rpim(I) all: 0.524 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.14)refinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fab BL3-6 4KZE, 3IVK
Resolution: 2.838→29.607 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.26
RfactorNum. reflection% reflection
Rfree0.2522 1718 4.04 %
Rwork0.1856 --
obs0.1856 42533 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.838→29.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6696 3934 0 180 10810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911256
X-RAY DIFFRACTIONf_angle_d1.1816184
X-RAY DIFFRACTIONf_dihedral_angle_d14.0036308
X-RAY DIFFRACTIONf_chiral_restr0.0551960
X-RAY DIFFRACTIONf_plane_restr0.0071366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8381-2.92150.37211350.30213208X-RAY DIFFRACTION96
2.9215-3.01570.33131410.28163347X-RAY DIFFRACTION100
3.0157-3.12340.36671430.25913387X-RAY DIFFRACTION100
3.1234-3.24830.29221410.21873370X-RAY DIFFRACTION100
3.2483-3.39590.32191430.20333380X-RAY DIFFRACTION100
3.3959-3.57470.24221420.18763395X-RAY DIFFRACTION100
3.5747-3.79820.23831410.17463351X-RAY DIFFRACTION100
3.7982-4.09080.21561440.16293406X-RAY DIFFRACTION100
4.0908-4.50120.22261430.15473415X-RAY DIFFRACTION100
4.5012-5.14960.22481450.14843444X-RAY DIFFRACTION100
5.1496-6.47670.24551460.1773482X-RAY DIFFRACTION100
6.4767-29.6090.25741540.17753630X-RAY DIFFRACTION100
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)
12.2866-0.2283-0.31970.6401-1.14581.9446-0.2525-0.57340.43430.34560.5698-0.0804-0.61940.2693-0.38341.3964-0.1424-0.1031.2299-0.2290.638117.869721.156855.3944
22.55090.01651.23940.68551.43635.43270.1015-0.87370.16610.24090.1716-0.3351-0.7043-0.5719-0.79081.9839-0.07580.17811.26170.01761.038113.380639.023551.5643
31.0943-0.8339-0.82241.0471.29392.32140.0154-0.76380.44590.55550.4105-0.3759-0.96910.1163-0.42721.61030.0392-0.10671.4191-0.20460.750918.388625.503161.1247
41.81151.23950.53193.22320.2291-0.1129-0.12940.49860.0334-0.27840.1409-0.45850.0498-0.1057-0.06940.7140.00690.0860.7179-0.0180.485417.665230.0226-6.4655
50.4741.5215-0.51376.1074-1.79630.85980.60960.53080.25980.8572-0.6627-1.86750.46190.4815-0.07391.0394-0.1545-0.14930.87810.14291.121517.857922.802617.6631
61.08820.05210.42821.27340.8451-0.216-0.01450.50730.079-0.22210.105-0.3936-0.05370.0553-0.21290.8254-0.02680.06890.78620.05940.483915.801617.912-12.616
70.31350.55520.40821.88872.15644.50990.2224-0.96350.65361.33420.1634-1.40350.32530.3638-0.42720.6817-0.1565-0.28570.704-0.18191.242234.47949.684320.1357
81.93060.52310.3744.4282.42544.8140.6699-0.13190.25320.0043-0.3916-1.6640.10070.6631-0.5660.5669-0.0551-0.08440.5668-0.01791.145535.310350.722811.8902
91.74980.7950.55643.52062.43724.76890.1175-0.38440.24080.40760.183-0.87960.00110.0732-0.2270.4868-0.0772-0.11430.51860.01730.996828.146649.053715.1187
100.65850.15450.08510.12920.44271.52390.5650.06940.18420.601-0.1058-0.6216-0.1760.7114-0.03731.5878-0.5157-0.81330.3933-0.50582.305234.88769.769938.7834
111.96020.51850.26346.01691.36625.1441.326-1.03190.37371.67430.3843-0.37250.3798-0.8904-0.16032.088-0.6099-0.36451.48280.29381.105519.573567.285451.076
121.22980.76-0.03633.08051.04081.61610.23870.2159-0.71030.48930.3543-1.08670.15710.41120.07872.3228-0.6263-0.77510.2713-0.71411.320829.67959.964139.4626
133.1169-1.80140.27433.29163.46066.1687-0.19460.1433-0.83211.9106-0.4888-0.85-0.01290.4495-0.08061.4589-0.0698-0.30020.747-0.02641.162323.163865.404438.9025
140.58470.20590.88752.93512.00113.24570.6216-0.6715-0.71572.3624-0.4381-0.81840.87420.37070.48142.778-0.5909-0.14320.83670.09731.037521.178160.919451.2631
150.58-0.81540.39385.50133.323.9570.8812-0.4043-0.2781.00750.7558-1.49951.17711.0536-0.45791.7443-0.4506-0.48921.3754-0.0571.435332.644261.651846.6312
161.4237-1.2267-0.29264.86922.60275.38610.41080.11510.48260.2085-0.33890.3258-0.5394-0.72750.09350.4915-0.0710.03640.60680.0370.68379.297952.907212.6694
171.5492-0.6229-0.42414.88181.75484.83230.3417-0.1590.61560.6688-0.42010.50271.26470.0252-0.03860.6111-0.1346-0.02450.56080.08410.679410.601545.344217.2262
181.3117-0.6348-0.84164.71382.56945.5750.0940.10221.11580.72160.5761-0.49420.6549-0.3348-0.10360.6143-0.0688-0.05870.49420.0280.753114.133451.453215.755
193.1303-2.53251.16232.81391.01575.5135-0.0037-0.81110.39251.61080.59080.2069-0.2822-1.05760.82231.338-0.33340.26990.7463-0.37380.80833.914960.677732.3545
201.92150.3041-1.01322.17692.5594.25221.0937-0.38220.5682.0787-0.2739-0.36280.2811-0.21780.02352.0093-0.2464-0.14730.66-0.12581.07916.788973.461745.2306
212.2370.3486-0.05575.88933.64355.72270.2660.18580.20241.61460.3485-0.5954-1.399-0.3838-0.11651.80130.20830.21850.96150.11160.892113.355171.073638.4381
220.74050.06120.5153.72362.43423.50880.0419-0.40420.88961.2928-0.2209-0.1030.0326-0.1517-0.05921.995-0.21760.00580.9169-0.20571.024114.620678.607947.8373
232.7390.2734-0.33564.15891.92366.42980.2332-0.1588-0.08680.27990.0884-0.8332-0.21350.7155-0.27750.5252-0.1105-0.12490.7853-0.10550.609632.93891.906732.9444
241.37670.7973-0.21771.89133.1617.8868-0.0018-0.5644-0.49110.36180.2178-0.0260.66630.8011-0.4950.58440.1840.05410.67230.05980.977134.3249-18.21359.0913
254.9515-2.07670.01155.96260.19966.63020.59080.64180.2993-0.5959-0.45190.07280.4996-0.4368-0.25160.50810.06570.06650.55140.08250.56418.9751-15.7645-2.7834
263.69110.83081.25122.60980.54935.3288-0.31150.010.4861-0.10810.2585-0.1262-0.25250.3461-0.06370.48910.06740.08750.44430.03850.67926.168-10.73822.9906
272.9121-0.19342.70923.30711.13446.83950.6811-0.5302-0.130.6579-0.40450.0420.86660.08370.14910.6614-0.1240.09260.61670.17220.33897.0322-3.689333.9525
282.35630.49371.5532.92741.50883.36340.0249-0.354-0.06080.31060.0012-0.1219-0.52480.05740.00790.5659-0.00140.01660.5859-0.01880.288211.75574.489332.1127
293.007-2.88-0.66913.03521.26498.3813-0.0259-0.9821-0.43521.48991.1644-1.41-0.3821-0.236-0.13640.7914-0.0192-0.11350.91870.11030.576720.07050.339742.0598
300.62641.40321.03934.03244.25116.78680.0642-0.0275-0.5483-0.24550.2842-0.24510.0237-0.42720.10510.50880.1050.00550.4484-0.06630.45174.0501-8.48316.4931
312.8114-1.8403-0.17395.23721.99193.186-0.0613-0.094-0.0028-0.1280.3195-0.62460.28130.1742-0.1290.50310.00130.07340.32480.00490.471916.4532-21.91373.7842
324.5434-0.6365-0.4634.82691.53082.5781-0.03390.0321-0.431-0.59090.0754-0.06690.1470.0007-0.0460.569-0.05340.11190.43880.03220.430613.8643-24.44834.4602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 594 through 623 )
2X-RAY DIFFRACTION2chain 'A' and (resid 624 through 653 )
3X-RAY DIFFRACTION3chain 'A' and (resid 654 through 684 )
4X-RAY DIFFRACTION4chain 'B' and (resid 594 through 623 )
5X-RAY DIFFRACTION5chain 'B' and (resid 624 through 633 )
6X-RAY DIFFRACTION6chain 'B' and (resid 634 through 684 )
7X-RAY DIFFRACTION7chain 'C' and (resid 4 through 43 )
8X-RAY DIFFRACTION8chain 'C' and (resid 44 through 86 )
9X-RAY DIFFRACTION9chain 'C' and (resid 87 through 125 )
10X-RAY DIFFRACTION10chain 'C' and (resid 126 through 138 )
11X-RAY DIFFRACTION11chain 'C' and (resid 139 through 159 )
12X-RAY DIFFRACTION12chain 'C' and (resid 160 through 171 )
13X-RAY DIFFRACTION13chain 'C' and (resid 172 through 189 )
14X-RAY DIFFRACTION14chain 'C' and (resid 190 through 208 )
15X-RAY DIFFRACTION15chain 'C' and (resid 209 through 228 )
16X-RAY DIFFRACTION16chain 'D' and (resid 2 through 39 )
17X-RAY DIFFRACTION17chain 'D' and (resid 40 through 76 )
18X-RAY DIFFRACTION18chain 'D' and (resid 77 through 102 )
19X-RAY DIFFRACTION19chain 'D' and (resid 103 through 114 )
20X-RAY DIFFRACTION20chain 'D' and (resid 115 through 151 )
21X-RAY DIFFRACTION21chain 'D' and (resid 152 through 173 )
22X-RAY DIFFRACTION22chain 'D' and (resid 174 through 214 )
23X-RAY DIFFRACTION23chain 'H' and (resid 4 through 125 )
24X-RAY DIFFRACTION24chain 'H' and (resid 126 through 138 )
25X-RAY DIFFRACTION25chain 'H' and (resid 139 through 159 )
26X-RAY DIFFRACTION26chain 'H' and (resid 160 through 228 )
27X-RAY DIFFRACTION27chain 'L' and (resid 2 through 26 )
28X-RAY DIFFRACTION28chain 'L' and (resid 27 through 91 )
29X-RAY DIFFRACTION29chain 'L' and (resid 92 through 102 )
30X-RAY DIFFRACTION30chain 'L' and (resid 103 through 114 )
31X-RAY DIFFRACTION31chain 'L' and (resid 115 through 151 )
32X-RAY DIFFRACTION32chain 'L' and (resid 152 through 214 )

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