[English] 日本語
Yorodumi
- PDB-6pzf: Crystal structure of human NA-63 Fab in complex with neuraminidas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pzf
TitleCrystal structure of human NA-63 Fab in complex with neuraminidase from A/Hunan/02650/2016(H7N9)
Components
  • NA-63 Fab heavy chain
  • NA-63 Fab light chain
  • Neuraminidase
KeywordsIMMUNE SYSTEM / antibody / inhibition mechanism
Function / homology
Function and homology information


exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / exo-alpha-(2->3)-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / integral component of membrane / metal ion binding
Sialidase superfamily / Neuraminidase / Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase - #10 / Neuraminidase / 6 Propeller / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
polysac:dmanpa1-2dmanpa1-2dmanpa1-3[dmanpa1-2dmanpa1-3[dmanpa1-2dmanpa1-6]dmanpa1-6]dmanpb1-4dglcpnacb1-4dglcpnacb1-: / Neuraminidase / polysac:dglcpnacb1-4dglcpnacb1-:
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhu, X. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI117905 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400024C United States
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Neuraminidase
A: Neuraminidase
E: NA-63 Fab light chain
F: NA-63 Fab heavy chain
L: NA-63 Fab light chain
H: NA-63 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,13717
Polymers184,0436
Non-polymers5,09411
Water1,36976
1
B: Neuraminidase
E: NA-63 Fab light chain
F: NA-63 Fab heavy chain
hetero molecules

B: Neuraminidase
E: NA-63 Fab light chain
F: NA-63 Fab heavy chain
hetero molecules

B: Neuraminidase
E: NA-63 Fab light chain
F: NA-63 Fab heavy chain
hetero molecules

B: Neuraminidase
E: NA-63 Fab light chain
F: NA-63 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,69040
Polymers368,08612
Non-polymers10,60428
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area51010 Å2
ΔGint-67 kcal/mol
Surface area117150 Å2
MethodPISA
2
A: Neuraminidase
L: NA-63 Fab light chain
H: NA-63 Fab heavy chain
hetero molecules

A: Neuraminidase
L: NA-63 Fab light chain
H: NA-63 Fab heavy chain
hetero molecules

A: Neuraminidase
L: NA-63 Fab light chain
H: NA-63 Fab heavy chain
hetero molecules

A: Neuraminidase
L: NA-63 Fab light chain
H: NA-63 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)377,85828
Polymers368,08612
Non-polymers9,77216
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area48720 Å2
ΔGint-42 kcal/mol
Surface area118520 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)164.576, 164.576, 192.575
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

-
Components

-
Protein , 1 types, 2 molecules BA

#1: Protein Neuraminidase /


Mass: 43982.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Hunan/02650/2016(H7N9)
Strain: A/Hunan/02650/2016(H7N9) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: R4NFR6*PLUS, exo-alpha-sialidase

-
Antibody , 2 types, 4 molecules ELFH

#2: Antibody NA-63 Fab light chain


Mass: 23547.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody NA-63 Fab heavy chain


Mass: 24491.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

-
Sugars , 3 types, 5 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1883.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1_j2-k1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 82 molecules

#7: Chemical ChemComp-CA / CALCIUM ION / Calcium


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Tris pH 9.0, 10% glycerol, 10% PEG6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2.8→49.8 Å / Num. obs: 63525 / % possible obs: 96.5 % / Redundancy: 8.4 % / CC1/2: 0.998 / Rpim(I) all: 0.06 / Rsym value: 0.17 / Net I/σ(I): 10
Reflection shellResolution: 2.8→2.85 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 2555 / CC1/2: 0.853 / Rpim(I) all: 0.35 / Rsym value: 0.98

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L14, 5IT2, 5V7R
Resolution: 2.8→49.8 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.96
RfactorNum. reflection% reflection
Rfree0.2486 3291 5.18 %
Rwork0.2031 --
Obs0.2055 63487 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12606 0 332 76 13014
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913315
X-RAY DIFFRACTIONf_angle_d1.25218189
X-RAY DIFFRACTIONf_dihedral_angle_d5.9839286
X-RAY DIFFRACTIONf_chiral_restr0.072052
X-RAY DIFFRACTIONf_plane_restr0.0082289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
2.7963-2.83620.44951030.34071968X-RAY DIFFRACTION77
2.8362-2.87850.38621150.32052070X-RAY DIFFRACTION81
2.8785-2.92350.37291050.31662137X-RAY DIFFRACTION83
2.9235-2.97140.3824960.32562277X-RAY DIFFRACTION88
2.9714-3.02270.33311260.30422380X-RAY DIFFRACTION92
3.0227-3.07760.37211470.32012446X-RAY DIFFRACTION96
3.0776-3.13680.37181340.30812517X-RAY DIFFRACTION98
3.1368-3.20080.33551160.28092574X-RAY DIFFRACTION99
3.2008-3.27040.29781580.26772534X-RAY DIFFRACTION99
3.2704-3.34650.29671550.25822556X-RAY DIFFRACTION100
3.3465-3.43010.30631340.2452610X-RAY DIFFRACTION100
3.4301-3.52290.28021450.22342554X-RAY DIFFRACTION100
3.5229-3.62650.2641340.22032595X-RAY DIFFRACTION100
3.6265-3.74350.24631580.21932563X-RAY DIFFRACTION100
3.7435-3.87730.24261310.19542605X-RAY DIFFRACTION100
3.8773-4.03240.23931190.17662614X-RAY DIFFRACTION100
4.0324-4.21590.22441610.1662570X-RAY DIFFRACTION100
4.2159-4.4380.18861500.15212604X-RAY DIFFRACTION100
4.438-4.71590.17411530.14442611X-RAY DIFFRACTION100
4.7159-5.07960.1891580.14012597X-RAY DIFFRACTION100
5.0796-5.59020.23331440.15762641X-RAY DIFFRACTION100
5.5902-6.39770.21411370.17592656X-RAY DIFFRACTION100
6.3977-8.05490.2471520.18582694X-RAY DIFFRACTION100
8.0549-49.80760.21751600.18892823X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refinement-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)
10.69440.1706-0.19411.1278-0.18611.538-0.0368-0.26140.15650.0757-0.10590.4526-0.1944-0.15410.18580.2486-0.01120.06440.3671-0.14270.742258.8963-0.988794.9821
20.7842-0.2633-0.97080.7124-0.64342.5108-0.1138-0.1551-0.2282-0.2562-0.07730.10230.1183-0.0360.25230.2309-0.01670.03070.3397-0.06110.765969.1582-10.877981.9494
30.585-0.1267-0.25770.9365-0.26981.1765-0.22620.05560.14270.04930.0221-0.16340.12950.05970.18420.284-0.03990.05670.2948-0.06280.712570.5765-10.003291.01
41.8679-1.06590.33981.05921.06583.7614-0.0307-0.0008-0.686-0.0197-0.09420.17170.1295-0.05220.07350.293-0.06010.17870.3299-0.0040.727669.9912-23.472994.3843
51.30070.26710.16521.54171.47433.46740.03870.123-0.24620.25960.1272-0.1550.4455-0.3412-0.0850.2681-0.06390.24590.4206-0.1310.870559.511-22.683894.593
61.89130.03410.77820.0676-0.35882.2777-0.13380.1382-0.24940.0424-0.30870.27560.4938-0.14210.32330.4349-0.15110.2370.4268-0.18910.968655.0501-26.231296.3484
73.78951.25251.02873.21980.53470.9151-0.06230.19250.00160.4844-0.2930.53520.474-0.6089-0.11620.2489-0.18570.17570.526-0.26461.009348.1705-16.222693.1538
81.32330.09791.36020.32750.67962.297-0.1865-0.1267-0.1947-0.0118-0.260.1993-0.04-0.34430.2170.2903-0.12490.16730.5815-0.29120.869842.5561-16.707392.354
91.45520.8378-0.01590.4573-0.21461.0915-0.21340.08570.12270.0282-0.08980.30080.2143-0.49360.23650.2815-0.03040.02560.4247-0.1840.772549.2212-7.124786.2534
102.6893-0.4868-1.60841.1011-0.12782.0495-0.14880.1924-0.072-0.133-0.21030.4709-0.1341-0.43470.32250.2384-0.0237-0.0220.34-0.14570.722857.43712.642180.8934
111.41370.4490.00891.19960.79221.0767-0.04050.3234-0.136-0.1150.1020.1091-0.0350.23990.03930.6435-0.01060.04910.48760.03220.40777.184-22.31275.3874
121.2508-0.68860.58991.5246-0.17430.89340.08250.274-0.0419-0.3182-0.00160.30050.0635-0.0205-0.16560.4715-0.0259-0.09460.5026-0.01320.225469.5001-10.373814.1419
131.1055-0.0557-0.31121.4713-1.06922.5691-0.05060.4539-0.2331-0.11070.22250.11370.294-0.0724-0.20190.5506-0.0537-0.14210.5342-0.04510.361255.8353-11.14837.1424
141.00050.39370.0551.9267-0.06630.8687-0.02150.3214-0.3122-0.24080.16490.30310.0184-0.1228-0.12730.6334-0.0892-0.16060.6115-0.06940.369556.5061-28.84986.4755
151.87310.22880.36252.16750.26020.86640.03480.1549-0.282-0.10460.0309-0.07460.171-0.058-0.08070.4078-0.04-0.04690.3984-0.04070.316273.4917-29.227914.7449
161.31140.2579-2.65712.7842-0.17735.4582-0.092-1.0381.5672-0.0435-0.07950.0334-0.4575-0.48710.27430.24850.0312-0.01821.3766-0.36751.346112.7542-8.691470.0606
170.7871-0.258-0.00543.4797-0.07852.0678-0.5428-0.67191.2003-0.4573-0.04120.7768-0.5259-1.19460.39340.3805-0.1569-0.23011.134-0.38511.37720.0941-7.980172.9392
186.06880.45181.19634.4902-1.08675.1375-0.4926-0.51191.0728-0.99250.18270.01550.2314-0.25560.09020.5282-0.19210.03880.5475-0.210.860727.7694-15.392569.3169
191.99060.339-1.36594.7392-0.35426.2064-0.1621-0.62241.3544-0.493-0.09310.6627-0.0406-1.18050.03220.3386-0.061-0.08250.8733-0.26351.05822.276-9.196167.9624
202.84160.06331.35141.25690.92274.9485-0.064-0.75561.1178-0.3184-0.13710.1978-0.7715-0.22650.19960.5053-0.15820.04490.7906-0.20441.028516.4412-13.897166.7378
214.41291.30870.48165.67120.58143.03430.099-0.05990.7618-0.2673-0.41280.0226-0.0148-0.1790.26730.6531-0.0994-0.20560.60040.10560.63926.1481-30.163742.1825
224.4541.19531.56133.31260.6812.9537-0.20910.64160.7729-0.52650.08670.3684-0.31830.17210.15940.737-0.102-0.06010.66450.08690.55333.2794-28.406642.9014
236.90683.8381.45054.05090.58235.5339-0.68041.04430.6777-1.74050.14430.22250.05230.30790.50440.95330.0546-0.23511.10670.23480.85375.6144-27.047232.8925
242.12750.5421.25213.3068-0.27112.90970.2454-1.06650.1925-0.3199-0.17220.25840.8193-0.9072-0.07220.502-0.8915-0.0091.4207-0.22010.674919.7255-30.744579.9661
251.5630.62491.66520.71510.52161.85450.9701-0.8483-0.0413-0.0345-0.5261-0.15730.5956-0.4816-0.28920.5741-0.3938-0.06080.86640.02020.594115.4519-35.740261.8332
261.6352-0.9355-1.42171.2234-1.1867.92-0.4335-0.2829-0.3068-0.026-0.2847-0.12421.05250.5640.37680.97640.0747-0.02890.66550.07321.097559.6949-65.92831.1556
271.6324-0.6264-0.84182.8599-0.90163.5810.1908-0.3329-0.4049-0.0959-0.1151-0.0855-0.0393-0.1337-0.09850.5515-0.0535-0.27560.6386-0.02360.837559.405-54.90929.2031
282.86430.8943-1.53880.8108-0.60285.1186-0.031-0.5314-0.28360.0356-0.0637-0.22430.19420.33810.15050.65010.1235-0.20310.60720.10030.920361.0457-56.375432.682
291.3010.3882-2.0391.4950.72514.55340.0687-0.5596-0.38780.12070.2914-0.25850.40980.5759-0.19460.71020.0396-0.2840.9051-0.05360.868355.0739-60.779234.1628
301.54560.75910.3261.57270.22431.57050.1084-1.1445-1.42120.69140.10110.0540.76980.2874-0.05331.0985-0.0715-0.24871.02940.57811.28235.7096-65.698858.0589
310.6765-0.5467-0.31761.08261.72963.5351-0.0825-1.4149-1.56810.647-0.07140.29071.0499-0.1458-0.0411.6178-0.1799-0.53191.1950.60891.459936.2208-75.2257.1904
326.40571.9431-0.13352.65230.23112.30640.2541-0.3839-1.05860.34650.03560.07380.2443-0.0209-0.21440.97760.0789-0.17480.90060.34250.941638.9687-64.191953.1469
332.69680.00690.02451.77960.93791.85440.1164-1.0037-1.04450.83260.03070.37040.9685-1.1073-0.39111.4281-0.3556-0.21391.91741.06181.532234.233-71.901864.8263
341.79820.74670.1151.8725-0.54741.68360.2651-1.2614-0.67840.7971-0.0842-0.15030.1617-0.5482-0.26791.7939-0.1429-0.26171.46140.77441.060638.3682-65.913267.7284
351.9249-0.5863-1.01121.6312-1.4773.19840.0904-0.0291-0.0846-0.0180.32460.7968-0.2106-0.683-0.24290.6830.0446-0.20020.73550.06130.996833.4645-56.272425.7616
363.6611.0868-0.46342.8396-1.6124.7277-0.23260.2262-0.0294-0.1060.26990.67440.1657-0.5741-0.09390.6779-0.1182-0.22620.5654-0.02490.772642.1652-55.996517.3918
374.19940.26520.87210.8555-0.66455.8941-0.38730.65160.1346-0.7450.65371.35560.6997-1.3263-0.3760.7417-0.2004-0.27190.86530.16740.755236.4814-58.857118.1408
383.62792.8943-3.03585.3666-3.64879.7664-0.330.5070.4635-0.43250.77110.3593-0.1655-0.4732-0.42960.5243-0.0953-0.08550.6082-0.10150.735248.7541-50.433322.334
391.90790.17440.08320.96990.40182.9061-0.10620.0689-0.15880.6085-0.00060.02880.061-0.04070.20310.8177-0.0486-0.05710.56220.20390.713430.7701-60.146345.381
402.50580.2995-0.04642.27790.51272.04360.0845-0.2935-0.13890.56020.1837-0.2343-0.0384-0.4767-0.3760.82820.0686-0.21890.70320.23890.86130.3686-52.614951.1093
413.8967-0.07060.87153.6791-1.91073.35950.4822-0.24870.3305-0.30710.46280.7048-0.7241-0.7486-0.57210.8040.1573-0.13680.62370.1341.03122.8597-53.117551.3886
Refinement TLS group
IDRefinement-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 83:111 )B83 - 111
2X-RAY DIFFRACTION2( CHAIN B AND RESID 112:157 )B112 - 157
3X-RAY DIFFRACTION3( CHAIN B AND RESID 158:190 )B158 - 190
4X-RAY DIFFRACTION4( CHAIN B AND RESID 191:218 )B191 - 218
5X-RAY DIFFRACTION5( CHAIN B AND RESID 219:246 )B219 - 246
6X-RAY DIFFRACTION6( CHAIN B AND RESID 247:280 )B247 - 280
7X-RAY DIFFRACTION7( CHAIN B AND RESID 281:302 )B281 - 302
8X-RAY DIFFRACTION8( CHAIN B AND RESID 303:338 )B303 - 338
9X-RAY DIFFRACTION9( CHAIN B AND RESID 339:440 )B339 - 440
10X-RAY DIFFRACTION10( CHAIN B AND RESID 441:468 )B441 - 468
11X-RAY DIFFRACTION11( CHAIN A AND RESID 83:112 )A83 - 112
12X-RAY DIFFRACTION12( CHAIN A AND RESID 113:190 )A113 - 190
13X-RAY DIFFRACTION13( CHAIN A AND RESID 191:232 )A191 - 232
14X-RAY DIFFRACTION14( CHAIN A AND RESID 233:353 )A233 - 353
15X-RAY DIFFRACTION15( CHAIN A AND RESID 354:468 )A354 - 468
16X-RAY DIFFRACTION16( CHAIN E AND RESID 1:14 )E1 - 14
17X-RAY DIFFRACTION17( CHAIN E AND RESID 15:38 )E15 - 38
18X-RAY DIFFRACTION18( CHAIN E AND RESID 39:61 )E39 - 61
19X-RAY DIFFRACTION19( CHAIN E AND RESID 62:90 )E62 - 90
20X-RAY DIFFRACTION20( CHAIN E AND RESID 91:113 )E91 - 113
21X-RAY DIFFRACTION21( CHAIN E AND RESID 114:150 )E114 - 150
22X-RAY DIFFRACTION22( CHAIN E AND RESID 151:198 )E151 - 198
23X-RAY DIFFRACTION23( CHAIN E AND RESID 199:214 )E199 - 214
24X-RAY DIFFRACTION24( CHAIN F AND RESID 1:60 )F1 - 60
25X-RAY DIFFRACTION25( CHAIN F AND RESID 61:228 )F61 - 228
26X-RAY DIFFRACTION26( CHAIN L AND RESID 1:14 )L1 - 14
27X-RAY DIFFRACTION27( CHAIN L AND RESID 15:61 )L15 - 61
28X-RAY DIFFRACTION28( CHAIN L AND RESID 62:90 )L62 - 90
29X-RAY DIFFRACTION29( CHAIN L AND RESID 91:113 )L91 - 113
30X-RAY DIFFRACTION30( CHAIN L AND RESID 114:150 )L114 - 150
31X-RAY DIFFRACTION31( CHAIN L AND RESID 151:163 )L151 - 163
32X-RAY DIFFRACTION32( CHAIN L AND RESID 164:186 )L164 - 186
33X-RAY DIFFRACTION33( CHAIN L AND RESID 187:198 )L187 - 198
34X-RAY DIFFRACTION34( CHAIN L AND RESID 199:214 )L199 - 214
35X-RAY DIFFRACTION35( CHAIN H AND RESID 1:16 )H1 - 16
36X-RAY DIFFRACTION36( CHAIN H AND RESID 17:63 )H17 - 63
37X-RAY DIFFRACTION37( CHAIN H AND RESID 64:95 )H64 - 95
38X-RAY DIFFRACTION38( CHAIN H AND RESID 96:106 )H96 - 106
39X-RAY DIFFRACTION39( CHAIN H AND RESID 107:184 )H107 - 184
40X-RAY DIFFRACTION40( CHAIN H AND RESID 185:215 )H185 - 215
41X-RAY DIFFRACTION41( CHAIN H AND RESID 216:228 )H216 - 228

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
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.

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