[English] 日本語
Yorodumi
- PDB-7nks: Structure of the Hantaan virus Gn glycoprotein ectodomain in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nks
TitleStructure of the Hantaan virus Gn glycoprotein ectodomain in complex with Fab HTN-Gn1
Components
  • Envelope polyprotein
  • Fab HTN-Gn1 heavy chain
  • Fab HTN-Gn1 light chain
KeywordsVIRAL PROTEIN / Hantaan virus glycoprotein / Gn glycoprotein / Fab / neutralizing antibody / viral glycoprotein in complex with antibody
Function / homology
Function and homology information


: / symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / virion membrane / signal transduction / membrane / metal ion binding
Similarity search - Function
: / Hantavirus glycoprotein Gn, base / Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / ITAM motif hantavirus type profile. / : / Hantavirus glycoprotein Gc, C-terminal ...: / Hantavirus glycoprotein Gn, base / Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / ITAM motif hantavirus type profile. / : / Hantavirus glycoprotein Gc, C-terminal / Hantavirus glycoprotein Gc / Hantavirus glycoprotein Gc, N-terminal
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesHantaan orthohantavirus
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsRissanen, I. / Bowden, T.A. / Huiskonen, J.T. / Stass, R.
Funding support United Kingdom, Finland, United States, 11items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/L009528/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S007555/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N002091/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/K024426/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC/PC/15068 United Kingdom
Academy of Finland309605 Finland
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R41AI132047 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R41AI132047-01S1 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R43AI142911 United States
Wellcome Trust203141/Z/16/Z United Kingdom
Wellcome Trust093305/Z/10/Z United Kingdom
CitationJournal: mBio / Year: 2021
Title: Structural Basis for a Neutralizing Antibody Response Elicited by a Recombinant Hantaan Virus Gn Immunogen.
Authors: Ilona Rissanen / Stefanie A Krumm / Robert Stass / Annalis Whitaker / James E Voss / Emily A Bruce / Sylvia Rothenberger / Stefan Kunz / Dennis R Burton / Juha T Huiskonen / Jason W Botten / ...Authors: Ilona Rissanen / Stefanie A Krumm / Robert Stass / Annalis Whitaker / James E Voss / Emily A Bruce / Sylvia Rothenberger / Stefan Kunz / Dennis R Burton / Juha T Huiskonen / Jason W Botten / Thomas A Bowden / Katie J Doores /
Abstract: Hantaviruses are a group of emerging pathogens capable of causing severe disease upon zoonotic transmission to humans. The mature hantavirus surface presents higher-order tetrameric assemblies of two ...Hantaviruses are a group of emerging pathogens capable of causing severe disease upon zoonotic transmission to humans. The mature hantavirus surface presents higher-order tetrameric assemblies of two glycoproteins, Gn and Gc, which are responsible for negotiating host cell entry and constitute key therapeutic targets. Here, we demonstrate that recombinantly derived Gn from Hantaan virus (HTNV) elicits a neutralizing antibody response (serum dilution that inhibits 50% infection [ID], 1:200 to 1:850) in an animal model. Using antigen-specific B cell sorting, we isolated monoclonal antibodies (mAbs) exhibiting neutralizing and non-neutralizing activity, termed mAb HTN-Gn1 and mAb nnHTN-Gn2, respectively. Crystallographic analysis reveals that these mAbs target spatially distinct epitopes at disparate sites of the N-terminal region of the HTNV Gn ectodomain. Epitope mapping onto a model of the higher order (Gn-Gc) spike supports the immune accessibility of the mAb HTN-Gn1 epitope, a hypothesis confirmed by electron cryo-tomography of the antibody with virus-like particles. These data define natively exposed regions of the hantaviral Gn that can be targeted in immunogen design. The spillover of pathogenic hantaviruses from rodent reservoirs into the human population poses a continued threat to human health. Here, we show that a recombinant form of the Hantaan virus (HTNV) surface-displayed glycoprotein, Gn, elicits a neutralizing antibody response in rabbits. We isolated a neutralizing (HTN-Gn1) and a non-neutralizing (nnHTN-Gn2) monoclonal antibody and provide the first molecular-level insights into how the Gn glycoprotein may be targeted by the antibody-mediated immune response. These findings may guide rational vaccine design approaches focused on targeting the hantavirus glycoprotein envelope.
History
DepositionFeb 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 15, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entity_branch_descriptor / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Envelope polyprotein
C: Fab HTN-Gn1 heavy chain
D: Fab HTN-Gn1 light chain
H: Fab HTN-Gn1 heavy chain
L: Fab HTN-Gn1 light chain
A: Envelope polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,12412
Polymers175,1576
Non-polymers2,9686
Water0
1
B: Envelope polyprotein
C: Fab HTN-Gn1 heavy chain
D: Fab HTN-Gn1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3118
Polymers87,5783
Non-polymers1,7335
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-17 kcal/mol
Surface area33890 Å2
MethodPISA
2
H: Fab HTN-Gn1 heavy chain
L: Fab HTN-Gn1 light chain
A: Envelope polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8134
Polymers87,5783
Non-polymers1,2351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-18 kcal/mol
Surface area34160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.022, 158.630, 70.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 21 through 34 or resid 37...
21(chain B and (resid 21 through 264 or resid 271 through 371))
12(chain C and resid 3 through 221)
22(chain H and resid 3 through 221)
13(chain D and resid 2 through 216)
23chain L
14chain F
24chain G

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNSERSER(chain A and (resid 21 through 34 or resid 37...AF21 - 346 - 19
121GLUGLUHISHIS(chain A and (resid 21 through 34 or resid 37...AF37 - 19822 - 183
131SERSERASPASP(chain A and (resid 21 through 34 or resid 37...AF205 - 281190 - 266
141SERSERGLUGLU(chain A and (resid 21 through 34 or resid 37...AF291 - 371276 - 356
211ASNASNPHEPHE(chain B and (resid 21 through 264 or resid 271 through 371))BA21 - 2646 - 249
221THRTHRGLUGLU(chain B and (resid 21 through 264 or resid 271 through 371))BA271 - 371256 - 356
112GLNGLNCYSCYS(chain C and resid 3 through 221)CB3 - 2213 - 221
212GLNGLNCYSCYS(chain H and resid 3 through 221)HD3 - 2213 - 221
113GLYGLYASPASP(chain D and resid 2 through 216)DC2 - 2162 - 216
213GLYGLYASPASPchain LLE2 - 2162 - 216
114NAGNAGMANMANchain FFH1 - 7
214NAGNAGMANMANchain GGG1 - 7

NCS ensembles :
ID
1
2
3
4

-
Components

-
Antibody , 2 types, 4 molecules CHDL

#2: Antibody Fab HTN-Gn1 heavy chain


Mass: 24284.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): H293T / Production host: Homo sapiens (human)
#3: Antibody Fab HTN-Gn1 light chain


Mass: 22943.162 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: pHLsec / Cell line (production host): H293T / Production host: Homo sapiens (human)

-
Protein / Non-polymers , 2 types, 5 molecules BA

#1: Protein Envelope polyprotein / M polyprotein


Mass: 40350.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hantaan orthohantavirus / Plasmid: pHLsec / Cell line (production host): H293T / Production host: Homo sapiens (human) / References: UniProt: A0A077D153
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C3H8O3

-
Sugars , 3 types, 3 molecules

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


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1WURCSPDB2Glycan 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]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.39 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES/MOPS pH 7.5, 0.12 M monosaccharides (glucose, mannose, galactose, fucose, xylose, NAG) and 30% ppt2 (ethylene glycol and polyethylene glycol 8000)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.5→62.22 Å / Num. obs: 33293 / % possible obs: 99.66 % / Redundancy: 12.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.042 / Rrim(I) all: 0.151 / Net I/σ(I): 12.1
Reflection shellResolution: 3.5→3.625 Å / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3252 / CC1/2: 0.94 / Rpim(I) all: 0.204 / % possible all: 98.81

-
Processing

Software
NameVersionClassification
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
DIALSdata scaling
PHENIX1.19phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OPG, 5M63

5opg

5m63


Resolution: 3.5→57.01 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2739 1676 5.04 %
Rwork0.2237 31546 -
obs0.2262 33222 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 332.73 Å2 / Biso mean: 124.9756 Å2 / Biso min: 48.68 Å2
Refinement stepCycle: final / Resolution: 3.5→57.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11662 0 198 0 11860
Biso mean--150.33 --
Num. residues----1550
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1948X-RAY DIFFRACTION9.3TORSIONAL
12B1948X-RAY DIFFRACTION9.3TORSIONAL
21C1318X-RAY DIFFRACTION9.3TORSIONAL
22H1318X-RAY DIFFRACTION9.3TORSIONAL
31D1292X-RAY DIFFRACTION9.3TORSIONAL
32L1292X-RAY DIFFRACTION9.3TORSIONAL
41F124X-RAY DIFFRACTION9.3TORSIONAL
42G124X-RAY DIFFRACTION9.3TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.60.3361260.31822574270099
3.6-3.720.34641370.283425932730100
3.72-3.850.34421380.26625702708100
3.85-4.010.3221440.266225792723100
4.01-4.190.34631410.245525982739100
4.19-4.410.27231020.202726552757100
4.41-4.690.26231570.184425712728100
4.69-5.050.23941560.191726132769100
5.05-5.550.23381300.196726452775100
5.55-6.360.2641490.226826552804100
6.36-8.010.30461510.240726772828100
8.01-57.010.22731450.20672816296199
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)
13.42320.4607-4.09243.27861.17895.8289-0.25180.8899-1.0506-0.3116-0.3303-0.38650.37420.58280.41650.77730.06750.07491.39930.10160.67985.5597-26.0145-8.0234
21.95750.813-2.09311.4691-0.91982.4927-0.48690.6249-0.3842-0.31760.1597-1.110.12871.80170.48140.8396-0.05050.28462.29680.00421.4247100.6526-21.9672-12.8492
34.81010.1265-2.41817.5944-3.00762.3573-0.6409-0.11770.59360.41720.2117-1.2994-0.62052.14240.15470.7898-0.3553-0.0981.9310.22661.047100.5613-8.4989-4.4036
45.6275-0.8008-1.66213.18620.74140.57-0.2660.19570.77430.16290.18920.234-0.35740.07850.07680.689-0.13190.00640.98530.13580.563985.65-11.7124-5.3626
58.34230.87391.37153.4560.92966.122-0.07662.00360.8491-0.506-0.56621.0344-0.2956-0.690.68780.51210.2027-0.03111.59940.05230.686149.8776-26.1818-10.5137
66.40763.326-0.4237.99691.29148.4552-0.1431.6611-0.4433-0.34130.1851-0.92590.20690.63530.13810.41560.16030.08431.2195-0.13270.586959.5631-31.9794-9.5639
72.8362-0.48070.28742.3917-0.65563.586-0.02731.161-0.4819-0.3661-0.6043-0.12360.21520.01030.50170.65610.2568-0.04611.8466-0.15880.514349.0019-31.7408-10.249
80.20250.7799-0.55083.5053-1.87756.2629-0.09590.66540.00320.630.60270.5269-0.0711-0.68370.22860.6507-0.00010.03062.0222-0.20720.366719.984-32.05961.9904
90.17250.34840.54380.9261-0.01897.0790.03341.0921-0.5982-0.2730.1615-0.33721.29440.477-0.87580.94480.1536-0.41441.8976-0.73210.565331.4874-43.1573-1.8689
100.76850.4518-1.09522.4598-1.46226.79720.23640.98280.2057-0.140.52380.2501-0.5601-1.23350.30910.750.0411-0.00012.37310.04870.5418.1309-29.2146-2.2408
115.7659-1.4796-4.96652.39512.41666.33350.0979-2.2437-0.25040.4522-0.1459-0.67910.0269-0.01040.06950.49960.0446-0.03531.21170.04660.779653.3895-35.378515.9694
125.6111-0.4672-5.32317.7078-0.63815.87930.0946-0.724-1.3983-0.7938-1.2755-1.0225-1.18170.59161.11650.64170.021-0.05061.24530.06120.597164.2151-32.317311.8725
136.4001-0.4355-1.52446.6322-2.30621.412-0.2373-0.23370.53280.4934-0.0614-0.3096-0.3124-0.89360.28550.70210.1221-0.05871.3168-0.17130.448654.9255-24.493712.065
145.5839-0.286-0.52630.82970.19431.32740.402-0.01930.06510.1101-0.2753-0.0787-0.16510.054-0.01070.71590.0405-0.06831.3787-0.09320.526442.4878-33.61679.2045
151.98493.20373.08257.92293.08916.37090.0870.8498-0.7391-0.9701-0.07891.10850.16290.0216-0.120.67320.1187-0.16211.2184-0.3580.718724.7054-43.10612.6791
163.75654.68821.89046.60121.87584.73680.32880.6644-0.195-0.061-0.242-0.13110.10170.9425-0.14830.65740.2115-0.10541.0397-0.20620.646926.1014-44.0519.015
178.45381.83735.95025.76290.35867.2986-0.08060.6502-1.951-0.3091-0.1920.14210.7233-0.95070.16650.726-0.1074-0.01431.3846-0.23870.837216.0561-47.978914.2421
186.67691.9328-1.44072.272-1.11461.93520.1437-1.0586-0.00630.2184-0.6309-0.46950.3958-0.02410.14740.5385-0.34880.0392.3180.16680.8136-6.2348-31.145-11.4671
198.1382-2.3831-0.41694.219-2.84925.80750.697-1.50481.47730.324-0.5533-0.8930.11020.5689-0.16430.6565-0.34490.17361.5069-0.0950.6878-14.7971-24.2611-16.8765
202.4926-1.2406-1.2253.7184-0.27714.5130.2496-1.6164-0.11660.7668-0.30680.7871-0.7726-0.0297-0.42790.6769-0.62840.17262.3447-0.16770.9156-18.745-28.7916-10.6825
214.6555-4.50691.83388.811-1.17671.85610.9778-0.25790.3487-0.011-1.83230.354-0.12070.22760.86270.6708-0.16570.02382.053-0.08620.6925-14.5378-23.0034-21.2271
222.3789-0.6411-1.63820.96911.87264.8463-0.0928-0.4076-0.85840.0992-0.0263-0.03760.49830.2919-0.00250.7512-0.1126-0.02411.75360.34450.563316.584-37.0639-23.5841
230.953-1.1076-0.9621.23841.46195.72860.4731-0.94380.2228-0.04520.9461-0.3927-0.03760.0493.22010.7234-0.13440.20462.65840.4314-0.21915.5928-31.4086-22.8642
240.70071.3638-1.91476.3968-0.38978.1175-0.14510.94550.3259-0.2838-0.49540.66140.0121-0.73980.35330.63470.0546-0.10881.9540.03650.4086-15.5077-31.651-41.8375
259.91272.0194-0.79377.04612.75763.45240.59920.3081.1160.2727-0.55360.5417-0.23380.5267-0.05980.64180.00790.10781.9952-0.01680.5783-17.2017-23.5887-32.4673
263.82560.5892-1.42411.82560.88171.46330.53820.2521.0538-0.3025-0.39590.235-0.2758-0.3974-0.09840.75110.13050.11462.20460.2770.7326-17.4637-22.0064-37.9636
270.59860.00451.3351.7035-0.10433.00380.63820.3432-0.017-0.0078-0.10470.2866-0.726-1.0936-0.47740.76550.0043-0.05861.55180.03790.3063-8.8274-31.4821-38.1663
286.8451-2.42583.23058.0065-1.76395.34810.1401-0.7582-0.98820.3545-0.0212-0.28930.1378-1.0531-0.30540.7508-0.254-0.10751.64220.12980.587714.0425-42.9543-33.5548
297.29210.91464.19925.29320.19663.403-0.29530.5966-1.2593-0.2995-0.01620.00860.12690.3171-0.01810.5158-0.01110.08590.9465-0.01350.546321.1428-48.2284-38.8216
303.9626-1.0968-3.92375.72020.06034.31250.46050.0805-0.4120.6395-0.33851.2173-0.6553-0.2673-0.34520.73-0.18770.22781.3621-0.17721.4845-65.5682-22.2849-6.5762
315.6534-0.5102-2.64354.6112-1.21944.83470.46550.6889-0.7214-0.24540.14780.47960.3585-0.06010.01620.7009-0.17650.17880.9575-0.05040.7681-52.6813-26.6812-16.887
324.824-2.9571-1.831.8191.29081.05390.09460.2095-0.1617-0.0137-0.09910.3485-0.2635-0.1086-0.0540.7429-0.05670.1421.2181-0.09920.8775-55.3695-16.92-15.2879
334.20210.05241.92060.90440.67381.75530.25121.42460.7052-0.9252-0.3026-0.8805-0.54170.94140.38691.47530.41210.52261.26280.70132.4635-57.6329-0.2983-28.2599
343.58140.101-0.52771.22581.33461.80680.72850.31991.3051-0.2496-0.49410.1446-0.83720.4712-0.33411.0859-0.09380.39980.709-0.02171.3595-49.1804-6.4571-17.5519
353.48732.57960.15183.29333.12827.31270.83680.09981.32050.21350.12770.7394-1.216-0.0593-0.44091.12750.01290.63750.4536-0.2231.776-42.154-10.1069-21.9468
362.348-0.07232.9522.81031.10744.22770.091-0.41290.32990.0574-0.2662-1.1615-0.8604-0.36680.13671.02810.0330.37650.4302-0.20871.4874-55.2889-3.1485-15.0077
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 20 through 106 )B20 - 106
2X-RAY DIFFRACTION2chain 'B' and (resid 107 through 229 )B107 - 229
3X-RAY DIFFRACTION3chain 'B' and (resid 230 through 275 )B230 - 275
4X-RAY DIFFRACTION4chain 'B' and (resid 276 through 372 )B276 - 372
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 41 )C1 - 41
6X-RAY DIFFRACTION6chain 'C' and (resid 42 through 70 )C42 - 70
7X-RAY DIFFRACTION7chain 'C' and (resid 71 through 128 )C71 - 128
8X-RAY DIFFRACTION8chain 'C' and (resid 129 through 173 )C129 - 173
9X-RAY DIFFRACTION9chain 'C' and (resid 174 through 185 )C174 - 185
10X-RAY DIFFRACTION10chain 'C' and (resid 186 through 221 )C186 - 221
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 19 )D1 - 19
12X-RAY DIFFRACTION12chain 'D' and (resid 20 through 34 )D20 - 34
13X-RAY DIFFRACTION13chain 'D' and (resid 35 through 76 )D35 - 76
14X-RAY DIFFRACTION14chain 'D' and (resid 77 through 134 )D77 - 134
15X-RAY DIFFRACTION15chain 'D' and (resid 135 through 155 )D135 - 155
16X-RAY DIFFRACTION16chain 'D' and (resid 156 through 191 )D156 - 191
17X-RAY DIFFRACTION17chain 'D' and (resid 192 through 216 )D192 - 216
18X-RAY DIFFRACTION18chain 'H' and (resid 3 through 18 )H3 - 18
19X-RAY DIFFRACTION19chain 'H' and (resid 19 through 53 )H19 - 53
20X-RAY DIFFRACTION20chain 'H' and (resid 54 through 93 )H54 - 93
21X-RAY DIFFRACTION21chain 'H' and (resid 94 through 114 )H94 - 114
22X-RAY DIFFRACTION22chain 'H' and (resid 115 through 150 )H115 - 150
23X-RAY DIFFRACTION23chain 'H' and (resid 151 through 222 )H151 - 222
24X-RAY DIFFRACTION24chain 'L' and (resid 2 through 26 )L2 - 26
25X-RAY DIFFRACTION25chain 'L' and (resid 27 through 50 )L27 - 50
26X-RAY DIFFRACTION26chain 'L' and (resid 51 through 98 )L51 - 98
27X-RAY DIFFRACTION27chain 'L' and (resid 99 through 119 )L99 - 119
28X-RAY DIFFRACTION28chain 'L' and (resid 120 through 191 )L120 - 191
29X-RAY DIFFRACTION29chain 'L' and (resid 192 through 216 )L192 - 216
30X-RAY DIFFRACTION30chain 'A' and (resid 21 through 38 )A21 - 38
31X-RAY DIFFRACTION31chain 'A' and (resid 39 through 73 )A39 - 73
32X-RAY DIFFRACTION32chain 'A' and (resid 74 through 214 )A74 - 214
33X-RAY DIFFRACTION33chain 'A' and (resid 215 through 248 )A215 - 248
34X-RAY DIFFRACTION34chain 'A' and (resid 249 through 310 )A249 - 310
35X-RAY DIFFRACTION35chain 'A' and (resid 311 through 344 )A311 - 344
36X-RAY DIFFRACTION36chain 'A' and (resid 345 through 371 )A345 - 371

+
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