[English] 日本語
Yorodumi
- PDB-6pcu: VP8* of a G2P[4] human rotavirus in complex with scFv antibody 9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pcu
TitleVP8* of a G2P[4] human rotavirus in complex with scFv antibody 9
Components
  • Outer capsid protein VP4
  • Variable domain of antibody scFv9
Keywordsviral protein/immune system / rotavirus / VIRAL PROTEIN / antibody / scFv / viral protein-immune system complex
Function / homology
Function and homology information


viral capsid / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane
Similarity search - Function
Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Outer capsid protein VP4
Similarity search - Component
Biological speciesRotavirus A
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHu, L. / Venkataram Prasad, B.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI36040 United States
Robert A. Welch FoundationQ1279 United States
CitationJournal: J.Clin.Invest. / Year: 2019
Title: Human VP8* mAbs neutralize rotavirus selectively in human intestinal epithelial cells.
Authors: Feng, N. / Hu, L. / Ding, S. / Sanyal, M. / Zhao, B. / Sankaran, B. / Ramani, S. / McNeal, M. / Yasukawa, L.L. / Song, Y. / Prasad, B.V.V. / Greenberg, H.B.
History
DepositionJun 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Dec 25, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_seq_id / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.end_auth_seq_id / _pdbx_refine_tls_group.selection_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_ref_seq_dif.align_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 2.1Oct 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
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer capsid protein VP4
B: Variable domain of antibody scFv9
D: Outer capsid protein VP4
E: Variable domain of antibody scFv9
G: Outer capsid protein VP4
H: Variable domain of antibody scFv9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,55916
Polymers133,6146
Non-polymers94510
Water9,476526
1
A: Outer capsid protein VP4
B: Variable domain of antibody scFv9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8225
Polymers44,5382
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-21 kcal/mol
Surface area17150 Å2
MethodPISA
2
D: Outer capsid protein VP4
E: Variable domain of antibody scFv9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1068
Polymers44,5382
Non-polymers5686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-41 kcal/mol
Surface area16910 Å2
MethodPISA
3
G: Outer capsid protein VP4
H: Variable domain of antibody scFv9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6303
Polymers44,5382
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-14 kcal/mol
Surface area16860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.428, 182.428, 193.753
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11D-435-

HOH

21D-449-

HOH

-
Components

#1: Protein Outer capsid protein VP4 / Indian G2P[4] rotavirus VP8*


Mass: 18498.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2VE61
#2: Antibody Variable domain of antibody scFv9


Mass: 26039.730 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM HEPES (pH 7.0) 20% w/v PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.4→35 Å / Num. obs: 63500 / % possible obs: 100 % / Redundancy: 13 % / Net I/σ(I): 10.83
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 12.6 % / Num. unique obs: 3131 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(DEV_3374: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VX4

5vx4


Resolution: 2.4→35 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.42
RfactorNum. reflection% reflection
Rfree0.237 3157 5 %
Rwork0.186 --
obs0.189 63183 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9184 0 54 526 9764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039441
X-RAY DIFFRACTIONf_angle_d0.71312827
X-RAY DIFFRACTIONf_dihedral_angle_d3.145504
X-RAY DIFFRACTIONf_chiral_restr0.0491397
X-RAY DIFFRACTIONf_plane_restr0.0051656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4023-2.43810.33781270.27312497X-RAY DIFFRACTION96
2.4381-2.47620.38581400.26392492X-RAY DIFFRACTION97
2.4762-2.51680.2761380.26312551X-RAY DIFFRACTION98
2.5168-2.56020.31291510.25712548X-RAY DIFFRACTION99
2.5602-2.60680.31191410.24972566X-RAY DIFFRACTION99
2.6068-2.65690.27941470.24062554X-RAY DIFFRACTION100
2.6569-2.71110.3551580.25322575X-RAY DIFFRACTION100
2.7111-2.770.34031530.25442598X-RAY DIFFRACTION100
2.77-2.83440.31741200.24682611X-RAY DIFFRACTION100
2.8344-2.90530.33661570.24052565X-RAY DIFFRACTION100
2.9053-2.98380.30711270.23182638X-RAY DIFFRACTION100
2.9838-3.07150.31191460.21412575X-RAY DIFFRACTION100
3.0715-3.17060.24291550.20542614X-RAY DIFFRACTION100
3.1706-3.28380.23691500.19342575X-RAY DIFFRACTION100
3.2838-3.41520.25511130.18792647X-RAY DIFFRACTION100
3.4152-3.57050.21961120.17182638X-RAY DIFFRACTION100
3.5705-3.75850.19531230.16062649X-RAY DIFFRACTION100
3.7585-3.99370.20181260.15782631X-RAY DIFFRACTION100
3.9937-4.30160.1831470.14212640X-RAY DIFFRACTION100
4.3016-4.73350.14491060.12682682X-RAY DIFFRACTION100
4.7335-5.41630.15921410.13862667X-RAY DIFFRACTION100
5.4163-6.81570.21441280.17392706X-RAY DIFFRACTION100
6.8157-35.00660.22271510.18042807X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.19074.0589-1.87576.1035-1.34142.28640.5369-0.855-0.3959-0.117-0.8391-0.54390.64251.3250.46330.43870.0274-0.05360.63970.14180.3263-42.79512.260854.7414
26.72345.14074.12864.19383.6993.42441.40470.9495-2.14390.5579-1.20950.20660.7335-0.4384-0.36310.52390.02580.00320.5533-0.16180.5451-42.49737.213227.466
37.51237.18172.54719.55526.00266.1656-0.7081.29461.1963-0.47020.4090.6822-0.86262.22630.15790.401-0.0784-0.01440.81980.19940.4708-22.295217.376431.4741
45.84456.38362.79576.96782.91272.1180.60280.6521-1.04460.1795-0.4252-1.3857-0.13140.6522-0.1240.29140.013-0.03590.69220.05480.4288-35.060614.393626.0534
51.9708-3.27092.95864.077-3.38817.2777-0.15660.09190.18370.0878-0.2682-0.2464-0.4632-0.41370.470.203-0.0327-0.00890.43450.02060.3245-43.068217.640832.2089
65.53632.38245.77017.32343.74816.1741-0.5721-0.530.23520.10640.4281-0.6553-1.4119-0.35010.21810.35910.0028-0.09040.42410.09570.5879-41.235427.288131.2395
78.90321.69365.13095.6991-1.27414.4481-0.42160.73520.3826-0.1827-0.3126-0.4788-0.27160.69020.59140.319-0.039-0.00310.55010.20830.4636-36.567621.239325.0066
87.49961.34592.0795.5357-0.21851.005-0.04540.66740.08650.2242-0.2518-0.8724-0.42940.4080.27710.3247-0.0589-0.05960.43820.08470.3613-35.707417.232435.06
93.18882.23152.23112.0454-0.0417.5448-0.4523-0.698-0.09840.25460.4502-0.32060.0035-1.0352-0.12130.4037-0.0482-0.08920.3433-0.03240.287-50.314612.693932.693
102.2818-0.4385-2.36333.4727-2.17688.24870.132-0.2337-1.2828-0.3034-0.5244-1.8802-1.6310.33440.4750.45380.0395-0.02530.38360.14010.5396-24.976713.251836.342
114.62591.90872.57211.66771.50883.4125-0.1526-0.07590.02920.2774-0.092-0.0325-0.35170.17510.24380.3570.07020.0010.2460.01660.2063-39.4374-22.90490.7895
120.9568-1.503-0.7343.18461.0652.3855-0.02690.1975-0.2394-0.0418-0.14340.77430.167-0.1130.20470.3111-0.0128-0.02020.3854-0.08230.3626-57.3384-27.03261.4244
131.6524-0.43820.7051.7262-0.11691.45990.08710.29260.0289-0.303-0.1339-0.12410.04270.02470.04630.27770.01690.02230.3239-0.00010.2292-46.3815-24.7756-6.7451
140.9132-1.12790.26212.17550.24798.6012-0.1553-0.3134-0.14970.0906-0.34040.2124-0.12050.19850.58880.18010.01340.00460.364-0.01640.3611-77.84411.459810.9831
153.4739-0.5902-1.39133.92062.93073.45020.0530.74060.04260.1308-0.304-0.38720.4443-0.8263-0.00060.23960.03040.0010.33410.05140.3156-78.4393-3.15739.7639
163.73280.1225-1.33553.72790.95382.47740.02630.03270.2309-0.1415-0.25290.1402-0.1242-0.3685-0.10240.2260.0475-0.03460.2839-0.01140.2354-69.4996-2.18278.0044
176.38563.10061.83124.19291.31373.3582-0.1171-0.0147-0.2793-0.09050.1840.4197-0.16130.2618-0.04720.32380.1067-0.00420.29870.00570.2463-67.4551-8.323311.3205
188.55664.02442.17695.32084.71299.33440.2245-1.0078-0.6281.0019-0.2897-0.04170.75350.819-0.08450.530.0464-0.00380.37170.07240.2958-65.7262-8.927420.5365
191.80152.54891.84944.13093.35552.7137-0.3882-0.15590.52880.2479-0.67490.53880.2617-0.42720.98250.38160.00690.02930.2908-0.01390.3921-76.3556-8.487711.3716
208.3423-2.3034-2.76673.7211-0.98187.7057-0.0198-1.3114-0.06632.23910.39990.2214-0.57540.3705-0.32490.7278-0.00310.0420.4969-0.06610.3391-74.7135-1.03926.6384
218.1209-3.64890.88148.06214.47653.9762-0.31420.1072-0.38340.0116-0.79780.6325-0.4876-0.21050.88910.268-0.04330.03830.2503-0.0020.2338-69.31090.52828.1216
228.3342-4.8232-6.24572.80143.61114.68170.31450.6698-0.1746-0.53110.0539-0.2140.24320.0783-0.08270.5059-0.0003-0.10450.4757-0.07390.3659-59.8475-3.3969-7.9507
231.58960.1251-2.4051.1281-0.01782.7879-0.4223-0.3155-0.3548-0.0482-0.05680.47070.12970.21680.15160.2390.0693-0.00750.38430.01630.3138-72.7383.914211.3817
245.24770.1380.8290.3184-0.62962.11310.3236-1.3226-0.44251.52670.0298-1.23260.07680.3823-0.34520.40660.0534-0.08910.6566-0.05230.7399-50.20964.256414.9919
253.7787-2.92484.58992.9627-5.0518.6263-0.41910.04491.4104-0.4216-0.2201-0.8803-0.73840.05460.69780.5432-0.11180.08990.27450.01750.756-53.764924.01483.3387
263.356-3.655-0.98246.25690.14842.8121-0.3625-0.3940.53930.35480.5106-0.8281-0.32940.1552-0.12140.2886-0.0208-0.03270.3659-0.06530.3454-50.67653.57456.8881
277.4139-5.3641-4.62215.78615.14584.8848-0.27280.29-0.20790.09780.0780.11240.3516-0.27360.090.28710.04670.00880.22690.09160.3024-61.35926.36092.5627
287.2354-2.5988-3.37814.51314.87565.98080.46580.13530.0351-1.29450.05630.0097-0.2004-0.1879-0.21930.323-0.03170.03610.24210.02950.2127-54.6344.3734-4.8838
294.9589-6.46352.39739.2039-3.28345.9140.2686-0.02660.16070.0081-0.11690.00860.5878-0.206-0.15050.4811-0.05390.07790.28110.01090.5008-51.37539.871-2.9894
307.1533-4.12223.18272.7704-3.19278.27251.01160.61630.7773-0.2669-0.8445-1.07560.09091.9056-0.00610.40320.1016-0.05520.47990.05580.7231-45.14888.23024.0189
312.7094-2.8390.31924.6221.19531.47240.42530.09950.2987-0.7541-0.2559-0.24270.17090.0708-0.05150.29730.0304-0.01140.31830.02770.3102-58.040210.71744.8228
322.2552-2.1321-0.20915.5893-0.52690.79860.12160.0689-0.22310.7144-0.08880.30690.34280.1603-0.20070.2606-0.0361-0.13530.3592-0.01080.3079-56.2426-3.572910.2698
333.62912.7001-1.51723.26351.51426.2063-0.5367-0.09850.48560.81810.9747-0.8637-1.2127-1.0609-0.14440.38450.1430.07740.3405-0.09250.4665-58.712321.877.7059
343.87321.743-0.70130.75660.05490.3648-0.18190.3221-0.0926-0.11230.0769-0.05860.0429-0.24550.12150.30310.0073-0.0110.3334-0.04910.2696-92.5466-24.4783-3.7422
353.366-2.421.32785.05062.69057.7409-0.1053-0.37530.0570.59311.0021-0.6059-0.01481.7063-0.85570.36520.0517-0.01210.5374-0.13170.3826-76.4497-30.86924.6436
363.939-1.3025-5.76650.92011.11578.5821-0.2528-0.46190.07760.13980.1062-0.15330.32280.40620.12960.3242-0.0252-0.02480.3741-0.06520.3305-79.9493-21.27283.0073
374.02631.9381-1.07284.2889-0.68472.6301-0.0971-0.0770.4230.08760.18520.08270.04490.3805-0.120.26270.03760.0230.2804-0.04350.349-90.3443-14.50981.7605
382.56710.1378-2.85572.81820.26024.4343-0.0640.04360.19380.13950.09240.203-0.1109-0.2542-0.02180.1920.0378-0.06670.2619-0.02820.2594-96.5154-19.1704-1.2939
398.5604-4.6289-3.94551.98894.75658.1707-0.52510.4342-0.39250.24110.72170.3054-0.22410.1134-0.10790.2447-0.0604-0.01550.2902-0.02550.1894-61.8683-26.1781-26.8045
403.7387-0.8229-0.49534.68260.88442.94640.0288-0.17910.06980.2187-0.0005-0.23230.12890.0705-0.0320.24430.0059-0.03030.24230.00270.1958-65.2042-36.0662-21.0882
412.22472.2542.97465.26956.47658.63190.51030.0409-0.87741.6157-0.1965-0.30621.07430.1083-0.20450.47910.00110.02150.36850.06420.328-71.7821-45.0932-15.8223
420.51351.52761.8613.48894.66486.2471-0.28240.2177-0.098-0.29920.914-0.27160.27460.4439-0.5610.30280.02880.02820.40560.00330.2586-60.9047-36.1208-16.0854
437.7831-2.75943.34573.72820.33512.27040.1859-0.0118-0.3578-0.72870.67170.89411.2580.2949-0.7140.50460.0274-0.1030.40550.01260.3383-62.8284-51.3254-23.3537
447.6957-8.4496-6.4469.86557.11956.2834-0.4258-0.28560.1320.16890.868-0.1971-0.1918-0.1063-0.42150.2503-0.0172-0.06020.3942-0.02140.2753-67.7236-32.7603-25.2377
452.2477-0.09881.43333.7313-5.07297.6432-0.4319-0.95512.0987-0.8257-0.27341.0072-2.4742-0.86170.96570.56930.0531-0.07560.5016-0.27250.8113-76.9192-16.3629-21.7512
465.5558-5.0293-1.2334.21271.55991.96330.27460.0657-0.3795-0.8343-0.2670.4159-0.0033-0.0829-0.11760.367-0.0501-0.00110.2687-0.02090.3071-64.2808-36.131-28.5581
476.03541.8571-2.47259.1521-5.2793.34720.3459-0.0665-0.7932-0.5157-0.02660.30681.0659-0.9732-0.36680.4473-0.0636-0.06380.5165-0.0910.4763-86.7279-39.5591-29.315
485.9236-0.4925-3.17011.72080.68785.38090.29791.08940.0715-0.317-0.3341-0.0466-0.1313-0.6685-0.02160.34730.1167-0.05520.4932-0.05620.328-84.7751-29.9654-43.6734
492.6089-1.9573-1.62531.6090.77682.2126-0.04930.23780.03430.00810.00080.1102-0.1649-0.2320.08560.30.0001-0.0250.358-0.03430.2268-81.2295-29.2628-28.2562
507.2261-0.0213-2.31713.61940.28083.26590.22390.17610.2771-0.042-0.2491-0.0382-0.7481-0.1365-0.1130.33910.0108-0.0430.3242-0.00210.2954-81.897-19.5093-29.5485
515.4822-3.6692-0.82732.59020.91338.1710.6545-0.71841.19660.37770.06030.0746-0.7147-0.1678-0.68740.49080.19240.00880.4287-0.0350.2622-85.4315-21.3618-35.269
523.22334.2104-4.01155.8767-5.40376.96781.33830.95960.53450.1776-0.07222.0359-0.5097-1.3893-1.05960.49710.1064-0.05980.66440.04180.6101-91.6882-28.4153-33.7107
531.94810.2553-4.16051.9712-0.81557.1520.25880.13730.38-0.3656-0.14320.40840.2545-0.1643-0.11280.28950.0747-0.04740.4038-0.03490.2962-78.6549-29.4605-35.7722
542.9650.1453-1.90950.1792-1.31847.8657-0.30360.0792-0.1559-0.07780.03580.02680.91380.34570.17780.2210.03820.0110.24060.00990.2928-80.7256-34.6237-21.3377
557.9406-2.37185.31397.0731-1.49823.5552-0.44951.3935-1.0027-0.9237-0.3615-0.27130.3242-1.02270.54260.34140.0976-0.04460.4397-0.15670.3325-78.3137-33.1748-45.5066
566.356-0.8470.51235.52191.59714.6173-0.03160.37940.2476-0.11620.05620.0251-0.2463-0.004-0.01370.30560.0162-0.00080.2531-0.00440.2548-68.029722.936314.6894
577.579-0.06231.26642.30470.67071.3398-0.1344-0.6259-0.00360.1865-0.01460.2536-0.0087-0.20150.16490.32210.0511-0.00130.4694-0.01860.241-73.058423.117932.4571
589.4417-0.45498.8313-0.0448-0.39677.9134-0.1511-0.75990.27460.2446-0.05930.2445-0.0571-0.64750.26590.41870.0384-0.00710.5141-0.15990.3699-68.22329.346433.9892
595.4954-0.10192.27672.24920.92092.1439-0.23310.08930.5332-0.1298-0.00510.0001-0.3707-0.07410.26280.38580.046-0.04620.35830.03290.268-70.1531.113318.3978
607.9298-1.29471.59880.70270.90223.2289-0.4668-0.75960.2641-0.12120.83880.0359-0.3303-0.3155-0.14780.55810.1084-0.18980.6038-0.20770.4651-45.028621.619351.3313
615.4357-3.41562.0046.9175-4.59126.7268-0.4834-1.3861-0.28550.60850.5749-0.3430.2255-0.8003-0.23340.540.08870.00030.71110.07790.3003-49.55596.773856.35
623.22490.5183-4.16056.6292-1.38038.3598-0.6085-0.77471.25271.40890.99140.4926-1.1845-0.8885-0.13750.73750.28570.0110.5037-0.0580.486-54.564226.392649.3153
636.8409-7.4668-2.20348.65852.41387.7547-0.6928-0.3916-0.36310.77660.45880.13030.430.01220.2290.26850.01660.02350.3834-0.02180.3247-47.89459.590344.0115
646.0469-4.00550.48873.00130.53657.4072-0.19850.6127-0.27090.3490.08490.02590.424-0.49760.10060.3504-0.01720.03080.37240.09130.3844-48.88127.818941.6149
654.88271.09414.08379.5951-1.43455.9280.029-0.77370.09930.63690.36581.3708-0.307-1.1429-0.22930.39380.16420.06430.57410.11540.505-60.421112.213743.569
668.2947-6.6284-6.69517.24386.91649.4291-0.47750.2201-1.34980.9786-0.68561.14370.1725-0.46420.93030.5638-0.14850.05690.54120.13970.5866-56.7955.007246.863
676.4415-0.86830.00988.67924.62613.1123-0.1669-0.8807-0.30761.14420.6979-0.0861-0.6298-0.7153-0.49890.58760.21150.05540.79470.14110.3614-54.995213.815653.3284
684.17855.7197-3.63749.3958-2.71956.7999-0.0405-0.5008-1.74730.14350.5463-0.25411.1132-0.377-0.44430.45080.0927-0.06050.73810.1750.6815-49.8436-3.402751.0072
693.1571-3.83330.21299.564-0.68930.19550.0925-0.37730.0810.3063-0.1981-0.2445-0.21490.16120.00790.40080.05050.02530.4530.01960.2943-46.742414.864445.7269
709.7202-5.57225.41234.3533-5.49918.54430.02510.20430.66330.4896-0.49810.0495-1.0949-0.30050.35210.46280.0962-0.09380.3922-0.08140.4533-46.630625.308540.4431
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 113:118 )H113 - 118
2X-RAY DIFFRACTION2( CHAIN H AND RESID 119:125 )H119 - 125
3X-RAY DIFFRACTION3( CHAIN H AND RESID 126:135 )H126 - 135
4X-RAY DIFFRACTION4( CHAIN H AND RESID 136:142 )H136 - 142
5X-RAY DIFFRACTION5( CHAIN H AND RESID 143:172 )H143 - 172
6X-RAY DIFFRACTION6( CHAIN H AND RESID 173:183 )H173 - 183
7X-RAY DIFFRACTION7( CHAIN H AND RESID 184:202 )H184 - 202
8X-RAY DIFFRACTION8( CHAIN H AND RESID 203:219 )H203 - 219
9X-RAY DIFFRACTION9( CHAIN H AND RESID 220:230 )H220 - 230
10X-RAY DIFFRACTION10( CHAIN H AND RESID 231:237 )H231 - 237
11X-RAY DIFFRACTION11( CHAIN A AND RESID 63:89 )A63 - 89
12X-RAY DIFFRACTION12( CHAIN A AND RESID 90:144 )A90 - 144
13X-RAY DIFFRACTION13( CHAIN A AND RESID 145:223 )A145 - 223
14X-RAY DIFFRACTION14( CHAIN B AND RESID 2:19 )B2 - 19
15X-RAY DIFFRACTION15( CHAIN B AND RESID 20:26 )B20 - 26
16X-RAY DIFFRACTION16( CHAIN B AND RESID 27:45 )B27 - 45
17X-RAY DIFFRACTION17( CHAIN B AND RESID 46:58 )B46 - 58
18X-RAY DIFFRACTION18( CHAIN B AND RESID 59:68 )B59 - 68
19X-RAY DIFFRACTION19( CHAIN B AND RESID 69:82 )B69 - 82
20X-RAY DIFFRACTION20( CHAIN B AND RESID 83:90 )B83 - 90
21X-RAY DIFFRACTION21( CHAIN B AND RESID 91:99 )B91 - 99
22X-RAY DIFFRACTION22( CHAIN B AND RESID 100:105 )B100 - 105
23X-RAY DIFFRACTION23( CHAIN B AND RESID 106:118 )B106 - 118
24X-RAY DIFFRACTION24( CHAIN B AND RESID 119:125 )B119 - 125
25X-RAY DIFFRACTION25( CHAIN B AND RESID 126:135 )B126 - 135
26X-RAY DIFFRACTION26( CHAIN B AND RESID 136:159 )B136 - 159
27X-RAY DIFFRACTION27( CHAIN B AND RESID 160:172 )B160 - 172
28X-RAY DIFFRACTION28( CHAIN B AND RESID 173:183 )B173 - 183
29X-RAY DIFFRACTION29( CHAIN B AND RESID 184:192 )B184 - 192
30X-RAY DIFFRACTION30( CHAIN B AND RESID 193:202 )B193 - 202
31X-RAY DIFFRACTION31( CHAIN B AND RESID 203:219 )B203 - 219
32X-RAY DIFFRACTION32( CHAIN B AND RESID 220:230 )B220 - 230
33X-RAY DIFFRACTION33( CHAIN B AND RESID 231:236 )B231 - 236
34X-RAY DIFFRACTION34( CHAIN D AND RESID 63:108 )D63 - 108
35X-RAY DIFFRACTION35( CHAIN D AND RESID 109:130 )D109 - 130
36X-RAY DIFFRACTION36( CHAIN D AND RESID 131:159 )D131 - 159
37X-RAY DIFFRACTION37( CHAIN D AND RESID 160:189 )D160 - 189
38X-RAY DIFFRACTION38( CHAIN D AND RESID 190:223 )D190 - 223
39X-RAY DIFFRACTION39( CHAIN E AND RESID 2:10 )E2 - 10
40X-RAY DIFFRACTION40( CHAIN E AND RESID 11:58 )E11 - 58
41X-RAY DIFFRACTION41( CHAIN E AND RESID 59:68 )E59 - 68
42X-RAY DIFFRACTION42( CHAIN E AND RESID 69:82 )E69 - 82
43X-RAY DIFFRACTION43( CHAIN E AND RESID 83:90 )E83 - 90
44X-RAY DIFFRACTION44( CHAIN E AND RESID 91:99 )E91 - 99
45X-RAY DIFFRACTION45( CHAIN E AND RESID 100:105 )E100 - 105
46X-RAY DIFFRACTION46( CHAIN E AND RESID 106:118 )E106 - 118
47X-RAY DIFFRACTION47( CHAIN E AND RESID 119:125 )E119 - 125
48X-RAY DIFFRACTION48( CHAIN E AND RESID 126:142 )E126 - 142
49X-RAY DIFFRACTION49( CHAIN E AND RESID 143:172 )E143 - 172
50X-RAY DIFFRACTION50( CHAIN E AND RESID 173:183 )E173 - 183
51X-RAY DIFFRACTION51( CHAIN E AND RESID 184:192 )E184 - 192
52X-RAY DIFFRACTION52( CHAIN E AND RESID 193:202 )E193 - 202
53X-RAY DIFFRACTION53( CHAIN E AND RESID 203:219 )E203 - 219
54X-RAY DIFFRACTION54( CHAIN E AND RESID 220:230 )E220 - 230
55X-RAY DIFFRACTION55( CHAIN E AND RESID 231:236 )E231 - 236
56X-RAY DIFFRACTION56( CHAIN G AND RESID 63:89 )G63 - 89
57X-RAY DIFFRACTION57( CHAIN G AND RESID 90:144 )G90 - 144
58X-RAY DIFFRACTION58( CHAIN G AND RESID 145:159 )G145 - 159
59X-RAY DIFFRACTION59( CHAIN G AND RESID 160:223 )G160 - 223
60X-RAY DIFFRACTION60( CHAIN H AND RESID 2:10 )H2 - 10
61X-RAY DIFFRACTION61( CHAIN H AND RESID 11:26 )H11 - 26
62X-RAY DIFFRACTION62( CHAIN H AND RESID 27:34 )H27 - 34
63X-RAY DIFFRACTION63( CHAIN H AND RESID 35:41 )H35 - 41
64X-RAY DIFFRACTION64( CHAIN H AND RESID 42:52 )H42 - 52
65X-RAY DIFFRACTION65( CHAIN H AND RESID 53:62 )H53 - 62
66X-RAY DIFFRACTION66( CHAIN H AND RESID 63:74 )H63 - 74
67X-RAY DIFFRACTION67( CHAIN H AND RESID 75:82 )H75 - 82
68X-RAY DIFFRACTION68( CHAIN H AND RESID 83:90 )H83 - 90
69X-RAY DIFFRACTION69( CHAIN H AND RESID 91:99 )H91 - 99
70X-RAY DIFFRACTION70( CHAIN H AND RESID 100:112 )H100 - 112

+
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