[English] 日本語
Yorodumi
- PDB-5moi: Crystal structure of human IgE-Fc epsilon 3-4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5moi
TitleCrystal structure of human IgE-Fc epsilon 3-4
ComponentsIg epsilon chain C region
KeywordsIMMUNE SYSTEM / immunoglobulin E / IgE / antibody
Function / homology
Function and homology information


adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / B cell antigen processing and presentation / type I hypersensitivity / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / Fc epsilon receptor (FCERI) signaling ...adaptive immune memory response / primary adaptive immune response / IgE B cell receptor complex / B cell antigen processing and presentation / type I hypersensitivity / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / type 2 immune response / immunoglobulin receptor binding / immunoglobulin complex, circulating / mast cell degranulation / B cell proliferation / macrophage differentiation / Role of LAT2/NTAL/LAB on calcium mobilization / complement activation, classical pathway / antigen binding / FCERI mediated Ca+2 mobilization / B cell receptor signaling pathway / FCERI mediated MAPK activation / FCERI mediated NF-kB activation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / immune response / inflammatory response / extracellular space / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Immunoglobulin heavy constant epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDore, K.A. / Davies, A.M. / Drinkwater, N. / Beavil, A.J. / McDonnell, J.M. / Sutton, B.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1100090 United Kingdom
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Thermal sensitivity and flexibility of the C epsilon 3 domains in immunoglobulin E.
Authors: Dore, K.A. / Davies, A.M. / Drinkwater, N. / Beavil, A.J. / McDonnell, J.M. / Sutton, B.J.
History
DepositionDec 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_unobs_or_zero_occ_atoms / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ig epsilon chain C region
B: Ig epsilon chain C region
C: Ig epsilon chain C region
D: Ig epsilon chain C region
E: Ig epsilon chain C region
F: Ig epsilon chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,96925
Polymers149,5216
Non-polymers6,44819
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.673, 90.296, 92.908
Angle α, β, γ (deg.)114.41, 90.63, 96.10
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Ig epsilon chain C region


Mass: 24920.146 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHE / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01854

-
Sugars , 4 types, 6 molecules

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


Type: oligosaccharide / Mass: 707.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3-3/a4-b1_b3-c1_b6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-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: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c6-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#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-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2-2/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 226 molecules

#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 25% (v/v) PEG1500, 0.1M SPG (succinic acid, sodium dihydrogen phosphate and glycine in the ratio 2:7:7)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→81.61 Å / Num. obs: 70275 / % possible obs: 98.9 % / Redundancy: 5.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.103 / Mean I/σ(I) obs: 2 / CC1/2: 0.656 / % possible all: 97

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HA0

3ha0


Resolution: 2.2→42.223 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 31.36
RfactorNum. reflection% reflection
Rfree0.2336 2992 4.98 %
Rwork0.2134 --
obs0.2144 60090 84.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→42.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8713 0 419 213 9345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039374
X-RAY DIFFRACTIONf_angle_d0.59112824
X-RAY DIFFRACTIONf_dihedral_angle_d13.9175676
X-RAY DIFFRACTIONf_chiral_restr0.041552
X-RAY DIFFRACTIONf_plane_restr0.0051586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23610.2622670.2521430X-RAY DIFFRACTION44
2.2361-2.27460.2859800.26111612X-RAY DIFFRACTION50
2.2746-2.3160.3402800.28911727X-RAY DIFFRACTION54
2.316-2.36050.3043890.27541959X-RAY DIFFRACTION60
2.3605-2.40870.26831100.26062031X-RAY DIFFRACTION64
2.4087-2.46110.31141310.26772245X-RAY DIFFRACTION70
2.4611-2.51830.37841120.27172449X-RAY DIFFRACTION75
2.5183-2.58130.28851380.26982581X-RAY DIFFRACTION81
2.5813-2.65110.31071580.25912890X-RAY DIFFRACTION88
2.6511-2.72910.28521510.25452954X-RAY DIFFRACTION94
2.7291-2.81710.30541470.25663238X-RAY DIFFRACTION99
2.8171-2.91780.28061600.25583156X-RAY DIFFRACTION100
2.9178-3.03460.23981720.2573214X-RAY DIFFRACTION100
3.0346-3.17270.28441530.2473257X-RAY DIFFRACTION100
3.1727-3.33990.28121830.23113177X-RAY DIFFRACTION100
3.3399-3.5490.25751590.22363214X-RAY DIFFRACTION100
3.549-3.82290.22211810.20593203X-RAY DIFFRACTION100
3.8229-4.20730.23291620.18263213X-RAY DIFFRACTION100
4.2073-4.81530.17691830.15783220X-RAY DIFFRACTION100
4.8153-6.06390.19142070.18043176X-RAY DIFFRACTION100
6.0639-42.23070.19771690.20173152X-RAY DIFFRACTION98
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)
16.76582.6838-0.33137.6001-0.53266.97270.20110.0946-0.00030.88190.0652-0.1923-0.24611.4603-0.28760.35320.0006-0.12330.34650.05670.521310.7222-41.489823.5882
25.25992.430.54595.8496-1.65310.82271.0948-1.7014-0.89652.236-0.4017-1.52020.56940.0801-0.19991.222-0.2059-0.29110.72630.1930.800312.192-45.951536.5368
34.47153.44092.55926.4643-0.18483.69950.9673-0.1284-1.08620.6185-0.2377-1.17070.16030.2587-0.16050.8486-0.0116-0.21170.07970.06720.666412.9519-46.825228.5486
44.10570.6882.62653.2227-1.38984.33850.6146-0.8563-1.13040.8883-0.38-0.29860.7852-0.3587-0.72830.7326-0.1074-0.10740.40750.12240.77694.379-50.561625.6506
54.6253-0.15130.38873.9778-0.84774.5887-0.05190.43120.6714-0.22620.2870.3268-0.1182-0.1466-0.14390.16030.03620.01360.1931-0.01950.33751.1503-27.26029.3659
65.46962.8619-2.08594.8257-2.13434.123-0.0391-0.2538-0.9830.1041-0.1058-0.09830.31510.4765-0.01820.26630.016-0.00260.2033-0.05730.42673.6352-31.101715.6154
74.87491.00120.01466.0274-1.82493.3343-0.0540.51261.1295-0.21590.0481-0.3617-0.23630.1771-0.00740.2006-0.00710.01370.25240.00490.42696.5633-24.66138.9133
87.0051.9209-1.06872.9293-4.69488.22240.11980.7144-0.4307-0.8633-0.0607-0.07510.62440.3782-0.05370.27230.00060.0140.3561-0.1560.26527.6827-36.77326.804
96.8671-0.045-0.53673.8907-1.93075.00610.3155-0.7129-0.77420.4962-0.057-0.0691-0.0197-0.4964-0.05130.3309-0.0769-0.04520.4879-0.16950.443-24.1931-23.901629.9691
106.19190.42440.83635.8749-2.13465.74950.4254-1.34-0.94740.4782-0.1770.06090.5309-0.37340.28580.4195-0.0854-0.0450.8949-0.04890.5237-28.5565-28.210335.7849
116.13450.2903-1.85362.4092-1.54384.16760.1801-0.98010.31010.769-0.3484-0.4368-0.7237-0.0206-0.07250.534-0.1223-0.06180.5641-0.23810.5267-22.2731-17.742532.2271
126.0187-1.19550.37026.91581.8955.97290.30930.48680.1006-0.6656-0.2624-0.0032-0.17690.07110.01730.21810.0319-0.00360.2204-0.01320.2364-13.4895-26.27717.6172
135.4383-0.1861-0.50276.66570.22333.80640.31850.29870.3093-0.4843-0.2013-0.16280.2087-0.8739-0.06530.5278-0.01520.00680.4819-0.06870.23826.2924-40.6276-17.1819
145.81911.736-0.2957.8083-0.63085.01190.2550.84131.0074-1.072-0.1836-0.3219-0.3795-0.2037-0.0460.50880.13440.10620.49930.02490.233210.4012-32.3966-20.3282
154.1003-0.7395-0.52633.3611-1.49075.43440.60840.70210.6104-0.4535-0.46040.0606-0.37640.6025-0.03590.58820.14290.09760.54180.03650.40513.0387-29.8087-16.8789
165.3121-0.7773-1.18593.6991-0.60186.37270.340.05140.85270.1582-0.18160.137-0.5825-0.3348-0.06330.4610.06630.1270.3723-0.01220.35778.2775-32.4774-11.5441
174.06131.43271.06754.78850.29620.28480.40420.8911-0.67970.2102-0.63630.53890.6725-0.33310.09560.38110.0561-0.10410.7433-0.18290.6093-2.411-56.6166-26.9156
182.39711.10660.80833.4541.58563.96620.28630.7842-0.6995-0.0835-0.149-0.2036-0.01380.1147-0.12870.4705-0.0071-0.09620.5847-0.21050.45233.6478-54.7424-27.5207
199.415-3.1806-1.80594.34974.03273.95361.0382-0.1909-0.1196-0.0113-0.5430.5355-0.4559-1.0499-0.32160.612-0.17930.04350.7631-0.18660.5951-9.5215-48.5673-20.6392
202.75330.55550.30342.32481.53535.18890.35960.84-1.52070.0283-0.1001-0.32570.39270.3491-0.17860.5369-0.0181-0.04880.706-0.35130.72354.4142-59.9513-28.6202
213.7895-1.3584-0.69193.3929-1.9674.95050.48022.10190.6337-0.5676-0.4206-0.0339-0.14490.3932-0.27790.5250.17070.03831.13430.24550.522-20.2101-35.1723-36.3554
222.3563-0.81190.9791.2435-0.70473.35130.7041.22250.8266-0.3716-0.34190.0196-0.8941-0.36510.77520.97950.35450.36831.27190.81590.8612-25.3462-22.7633-36.5513
232.3205-0.1034-1.10240.0275-0.1727.05080.92350.88951.4313-0.5275-0.4914-0.5243-0.31620.4578-0.00710.8650.31070.21931.24970.48440.5575-21.2943-28.6927-32.8702
243.6359-1.1659-0.51853.2753-0.02041.83890.23871.07-0.2452-0.9437-0.2722-0.62470.20830.1416-0.05240.48830.10920.04891.0109-0.22910.4253-10.5677-55.0579-35.5579
254.7408-1.2837-0.40293.4633-1.59153.9140.43511.4417-0.6109-0.5057-0.29920.416-0.157-0.369-0.09320.51940.1429-0.05520.9372-0.32580.435-16.4234-54.8587-35.2823
266.0654-2.3862-0.89035.3561.33938.8288-0.34-0.2436-0.5312-0.11020.4731-0.1240.15251.4993-0.19530.3623-0.03030.05450.42610.04480.454916.2868-67.3199-1.2531
277.5748-0.42330.10415.6974-0.70666.83880.49270.95240.1354-0.4871-0.211-1.4097-0.25251.3423-0.19580.5914-0.07340.14411.0446-0.08510.535323.5886-66.0675-12.5835
281.1899-1.68690.28692.4310.04364.98350.07420.6853-1.30110.01260.3720.49892.27290.8636-0.46411.41550.5108-0.2080.9091-0.14581.451120.9945-82.6147-6.0293
297.0612-1.21710.56278.65372.56498.2305-0.05940.2965-0.0342-1.27970.5837-0.4955-1.40331.6815-0.35740.6513-0.19010.04610.5898-0.05090.35319.4478-63.6545-7.6401
303.59430.1685-1.08041.3478-0.85977.44590.02810.47050.4178-0.9940.04070.0309-1.09940.5581-0.09810.58410.0116-0.02720.45170.11060.423610.3281-63.9886-8.9451
315.863.7404-3.15224.8518-5.94498.64180.1918-1.0051-0.50070.61260.64651.9673-0.177-1.0537-0.84020.3661-0.0130.00330.99840.17880.6297-1.4514-74.268423.0867
323.87072.1274-1.91482.30361.10355.05990.139-0.6216-0.68290.40620.1660.799-0.5994-0.5431-0.29340.1520.05050.04950.43830.13350.58471.1028-69.775716.6279
335.23790.34240.67836.3882-2.54442.1768-0.29870.37450.2454-0.3451-0.00090.2184-0.728-0.1322-0.09270.31370.00450.03890.26110.05910.30237.8493-64.52429.3813
345.9810.85121.6874.8277-0.90158.46180.0854-0.78-0.70480.4978-0.0111-0.4268-0.02720.47940.0320.20980.0166-0.01070.45030.13550.449413.904-72.051618.5935
352.26982.34980.94325.6966-1.442.1759-0.00490.65040.0052-1.0018-0.03321.1909-0.2747-0.9681-0.06190.49250.0833-0.11470.61550.07390.5705-3.2559-66.24613.1778
365.48450.22880.55054.2528-0.38337.04160.0201-1.3249-0.24050.46470.10320.1685-0.4083-0.4329-0.07840.24090.07550.06470.49160.06510.34527.2592-67.484920.0277
376.3675-0.5287-3.27246.9896-1.21467.4715-0.31520.3959-1.5347-1.1039-0.61170.6570.7231-0.78061.00240.53450.0168-0.03730.5742-0.13161.2146-13.8639-89.28890.5601
382.0806-0.94351.39030.4274-0.6310.92460.02421.0298-0.5687-1.5249-0.2622-0.4572.09360.8010.09161.35620.16260.10010.7897-0.5031.3627-12.1201-94.5495-11.5588
396.4066-1.78693.16178.4498-3.13626.96790.5211.1242-1.3466-1.0494-0.40730.27671.44710.1707-0.05840.93490.05150.17290.5331-0.10821.5154-10.9186-92.3837-9.0201
401.8267-0.79712.00043.044-2.42073.07670.24310.2346-2.4059-0.6433-0.3449-0.05031.20880.73160.28740.58040.2715-0.06340.71230.23691.8486-4.0414-95.55198.1576
416.8507-0.9904-0.56334.10670.51813.72540.1955-1.0495-0.64070.1218-0.3137-0.3724-0.00320.29570.03480.2227-0.0337-0.00260.58250.12090.6234-8.8868-74.03314.7286
426.3098-1.0876-0.60193.43491.33393.5685-0.3975-0.5594-0.78860.29710.1237-0.23460.3190.5752-0.03870.30840.1335-0.06080.50030.14110.6776-10.2482-77.20318.6031
436.9432-0.98160.60746.32860.05472.82960.11-1.0407-0.26120.1988-0.34910.2125-0.0771-0.09320.26150.2178-0.0449-0.03760.67520.14190.6579-14.2892-75.505215.4457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 339 through 354 )
2X-RAY DIFFRACTION2chain 'A' and (resid 355 through 399 )
3X-RAY DIFFRACTION3chain 'A' and (resid 400 through 411 )
4X-RAY DIFFRACTION4chain 'A' and (resid 412 through 443 )
5X-RAY DIFFRACTION5chain 'A' and (resid 444 through 480 )
6X-RAY DIFFRACTION6chain 'A' and (resid 481 through 502 )
7X-RAY DIFFRACTION7chain 'A' and (resid 503 through 527 )
8X-RAY DIFFRACTION8chain 'A' and (resid 528 through 544 )
9X-RAY DIFFRACTION9chain 'B' and (resid 338 through 376 )
10X-RAY DIFFRACTION10chain 'B' and (resid 377 through 398 )
11X-RAY DIFFRACTION11chain 'B' and (resid 399 through 443 )
12X-RAY DIFFRACTION12chain 'B' and (resid 444 through 544 )
13X-RAY DIFFRACTION13chain 'C' and (resid 336 through 349 )
14X-RAY DIFFRACTION14chain 'C' and (resid 350 through 370 )
15X-RAY DIFFRACTION15chain 'C' and (resid 371 through 396 )
16X-RAY DIFFRACTION16chain 'C' and (resid 397 through 433 )
17X-RAY DIFFRACTION17chain 'C' and (resid 434 through 458 )
18X-RAY DIFFRACTION18chain 'C' and (resid 459 through 492 )
19X-RAY DIFFRACTION19chain 'C' and (resid 493 through 502 )
20X-RAY DIFFRACTION20chain 'C' and (resid 503 through 544 )
21X-RAY DIFFRACTION21chain 'D' and (resid 335 through 361 )
22X-RAY DIFFRACTION22chain 'D' and (resid 362 through 385 )
23X-RAY DIFFRACTION23chain 'D' and (resid 386 through 433 )
24X-RAY DIFFRACTION24chain 'D' and (resid 434 through 458 )
25X-RAY DIFFRACTION25chain 'D' and (resid 459 through 544 )
26X-RAY DIFFRACTION26chain 'E' and (resid 336 through 361 )
27X-RAY DIFFRACTION27chain 'E' and (resid 362 through 384 )
28X-RAY DIFFRACTION28chain 'E' and (resid 385 through 396 )
29X-RAY DIFFRACTION29chain 'E' and (resid 397 through 421 )
30X-RAY DIFFRACTION30chain 'E' and (resid 422 through 443 )
31X-RAY DIFFRACTION31chain 'E' and (resid 444 through 458 )
32X-RAY DIFFRACTION32chain 'E' and (resid 459 through 469 )
33X-RAY DIFFRACTION33chain 'E' and (resid 470 through 479 )
34X-RAY DIFFRACTION34chain 'E' and (resid 480 through 492 )
35X-RAY DIFFRACTION35chain 'E' and (resid 493 through 502 )
36X-RAY DIFFRACTION36chain 'E' and (resid 503 through 544 )
37X-RAY DIFFRACTION37chain 'F' and (resid 339 through 354 )
38X-RAY DIFFRACTION38chain 'F' and (resid 355 through 384 )
39X-RAY DIFFRACTION39chain 'F' and (resid 385 through 433 )
40X-RAY DIFFRACTION40chain 'F' and (resid 434 through 443 )
41X-RAY DIFFRACTION41chain 'F' and (resid 444 through 480 )
42X-RAY DIFFRACTION42chain 'F' and (resid 481 through 502 )
43X-RAY DIFFRACTION43chain 'F' and (resid 503 through 544 )

+
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