[English] 日本語
Yorodumi
- PDB-6eyo: Structure of extended IgE-Fc in complex with two anti-IgE Fabs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6eyo
TitleStructure of extended IgE-Fc in complex with two anti-IgE Fabs
Components
  • 8D6 Fab heavy chain
  • 8D6 Fab light chain
  • Immunoglobulin heavy constant epsilon
KeywordsIMMUNE SYSTEM / Immunoglobulin E / Fab / antibody / complex
Function / homology
Function and homology information


IgE B cell receptor complex / adaptive immune memory response / primary adaptive immune response / type I hypersensitivity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / type 2 immune response ...IgE B cell receptor complex / adaptive immune memory response / primary adaptive immune response / type I hypersensitivity / B cell antigen processing and presentation / Fc receptor-mediated immune complex endocytosis / eosinophil degranulation / IgE immunoglobulin complex / macrophage activation / type 2 immune response / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / mast cell degranulation / B cell proliferation / macrophage differentiation / Role of LAT2/NTAL/LAB on calcium mobilization / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / complement activation, classical pathway / antigen binding / FCERI mediated MAPK activation / B cell receptor signaling pathway / FCERI mediated NF-kB activation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / inflammatory response / immune 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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsChen, J.B. / Ramadani, F. / Pang, M.O.Y. / Beavil, R.L. / Holdom, M.D. / Mitropoulou, A.N. / Beavil, A.J. / Gould, H.J. / Chang, T.W. / Sutton, B.J. ...Chen, J.B. / Ramadani, F. / Pang, M.O.Y. / Beavil, R.L. / Holdom, M.D. / Mitropoulou, A.N. / Beavil, A.J. / Gould, H.J. / Chang, T.W. / Sutton, B.J. / McDonnell, J.M. / Davies, A.M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1100090 United Kingdom
Asthma UKAUK-PG-2013-183 United Kingdom
Wellcome Trust085944 United Kingdom
CitationJournal: Sci Rep / Year: 2018
Title: Structural basis for selective inhibition of immunoglobulin E-receptor interactions by an anti-IgE antibody.
Authors: Chen, J.B. / Ramadani, F. / Pang, M.O.Y. / Beavil, R.L. / Holdom, M.D. / Mitropoulou, A.N. / Beavil, A.J. / Gould, H.J. / Chang, T.W. / Sutton, B.J. / McDonnell, J.M. / Davies, A.M.
History
DepositionNov 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
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 / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Immunoglobulin heavy constant epsilon
B: Immunoglobulin heavy constant epsilon
I: 8D6 Fab heavy chain
H: 8D6 Fab heavy chain
M: 8D6 Fab light chain
L: 8D6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,7358
Polymers169,4276
Non-polymers2,3082
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18740 Å2
ΔGint-44 kcal/mol
Surface area66380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.483, 119.601, 132.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Immunoglobulin heavy constant epsilon / Ig epsilon chain C region / Ig epsilon chain C region ND


Mass: 36354.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fc region of immunoglobulin E / Source: (gene. exp.) Homo sapiens (human) / Gene: IGHE / Cell line (production host): MOUSE MYELOMA NS0 / Production host: Mus musculus (house mouse) / References: UniProt: P01854
#2: Antibody 8D6 Fab heavy chain


Mass: 24555.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 8D6 Fab heavy chain / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody 8D6 Fab light chain


Mass: 23803.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 8D6 Fab light chain / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: 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
#5: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris-HCl pH8.0 and 45% (v/v) pentaerythritol propoxylate (5/4PO/OH)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.7→88.93 Å / Num. obs: 20732 / % possible obs: 98.8 % / Redundancy: 6.6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.224 / Rpim(I) all: 0.094 / Net I/σ(I): 6.8
Reflection shellResolution: 3.7→4.05 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4698 / CC1/2: 0.819 / Rpim(I) all: 0.284 / % possible all: 95.3

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wqr
Resolution: 3.7→88.93 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.25 / Phase error: 29.32
RfactorNum. reflection% reflection
Rfree0.2882 1125 5.44 %
Rwork0.2473 --
obs0.2496 20683 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.7→88.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10230 0 155 0 10385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210674
X-RAY DIFFRACTIONf_angle_d0.5114687
X-RAY DIFFRACTIONf_dihedral_angle_d11.5416261
X-RAY DIFFRACTIONf_chiral_restr0.041748
X-RAY DIFFRACTIONf_plane_restr0.0051866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7001-3.86850.34421080.3232220X-RAY DIFFRACTION91
3.8685-4.07240.33491510.28582413X-RAY DIFFRACTION100
4.0724-4.32760.33291330.26052464X-RAY DIFFRACTION100
4.3276-4.66170.27641400.22452432X-RAY DIFFRACTION100
4.6617-5.13080.24911520.22682447X-RAY DIFFRACTION100
5.1308-5.87310.25691420.23352455X-RAY DIFFRACTION100
5.8731-7.39890.31031430.2592522X-RAY DIFFRACTION100
7.3989-88.95550.27641560.23122605X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0723-0.0114-0.00050.04620.0047-0.00380.01290.02060.093-0.0307-0.0062-0.0049-0.0542-0.0313-0.03250.20620.28240.05470.06010.05230.069814.4946-60.332819.3387
20.04630.05470.07260.05590.07670.09890.11160.0822-0.17370.016-0.0108-0.068-0.1352-0.04640.01980.22270.02270.06230.34350.1380.3655-16.9842-84.911622.2831
30.07930.0195-0.04210.02730.01660.047-0.0292-0.0856-0.1008-0.4469-0.02450.26880.1592-0.1648-0.00010.5770.1513-0.0250.68830.18290.701-23.181-91.989517.1848
40.021-0.0202-0.02750.03270.02870.026-0.0541-0.2957-0.0892-0.1863-0.015-0.0027-0.0087-0.2038-00.43410.01260.03810.58980.06140.4644-30.0893-109.080920.3943
50.2847-0.1277-0.12260.10390.11360.11720.07280.00120.0921-0.02180.0843-0.074-0.05430.13990.4189-0.01120.29920.11890.2735-0.22930.06727.238-76.200916.2891
60.1023-0.01810.03450.0604-0.07420.1174-0.1091-0.0896-0.22790.22060.2394-0.04290.1148-0.07690.32250.40070.1428-0.16440.32690.01080.6167-5.2054-114.98029.7936
70.00220.0012-0.00010.0005-0.00120.0008-0.0042-0.0850.03630.0102-0.0518-0.1177-0.0320.1267-0.08620.2154-0.21550.05210.5471-0.03450.24924.7898-82.4511-13.0605
80.010.00880.00670.00510.00530.0057-0.00180.0206-0.0143-0.01710.0133-0.00360.0120.0324-0.06450.14860.1528-0.08670.4374-0.28680.3077-0.2347-91.0356-11.4042
90.22550.0637-0.20170.4609-0.16360.3174-0.1182-0.0069-0.14670.0692-0.1239-0.06710.03220.058-0.40930.1414-0.06550.08590.4425-0.07410.22380.4018-78.3586-19.4836
100.01430.00650.00290.0143-0.01160.0134-0.2192-0.05840.1711-0.0476-0.0897-0.1098-0.12590.128301.2841-0.14320.01540.5435-0.02990.9633-2.5446-59.8278-27.2393
110.00080.0030.00180.01990.0090.0044-0.03350.02520.0209-0.05410.0288-0.0018-0.0480.0296-0.00910.5499-0.2566-0.02040.3759-0.16680.39773.1496-83.129656.11
120.09040.01730.03930.00920.00310.0195-0.0716-0.05490.02370.04760.1092-0.0344-0.0118-0.04690.02770.3489-0.0466-0.02190.3349-0.0560.09181.9893-83.533442.6327
130.00770.00270.01010.0030.00070.02250.0263-0.00450.02050.0010.03060.0038-0.0213-0.04510.1150.0379-0.02870.04150.09360.07970.2341-1.3965-95.323448.9959
140.20190.0580.18850.1546-0.0360.23390.1522-0.0281-0.04310.0684-0.04330.0631-0.0008-0.02010.08240.26270.0123-0.03520.1867-0.16390.3778-7.0959-83.932643.7668
15-0.001-0.000700.0015-0.00330.00210.0164-0.0210.0614-0.0482-0.0035-0.031-0.0243-0.004800.58850.0462-0.01620.65450.12480.4936-4.473-86.062556.0724
160.00610.00580.00220.009-0.00360.00760.0226-0.00790.18150.0843-0.0404-0.0980.00050.08760.00010.4070.01850.01040.35880.1290.39764.6963-90.216238.9764
170.00060.0022-0.00230.0029-0.0010.0021-0.0307-0.05610.03540.0220.0143-0.030.0013-0.053200.8607-0.11570.0520.61140.07120.6145.23-85.753964.2743
180.00320.00040.0010.00310.00570.0078-0.0655-0.02640.06880.0492-0.15940.0447-0.0454-0.0203-00.8349-0.2069-0.20710.6814-0.24361.101825.9227-90.282672.1335
190.002-0.00080.0005-0.00150.0001-0.0008-0.00890.0091-0.00820.060.027-0.0643-0.04450.0019-01.04440.1016-0.22260.74550.19430.786821.7333-88.238262.3398
200.01-0.0083-0.00090.0035-0.0050.001-0.061-0.06880.07740.0793-0.05560.1483-0.0277-0.0926-01.0836-0.3045-0.08850.61940.00610.896818.7028-89.666968.1212
210.0021-0.0020.00070.0005-0.0004-0.00040.04560.02040.00190.00850.026-0.0319-0.0253-0.0224-01.11350.1715-0.11441.02950.04921.020527.2723-82.140871.2929
220.03280.0110.02510.00280.00650.02770.03140.0706-0.061-0.02240.04640.01340.0482-0.0570.02960.15420.1243-0.16770.2539-0.05340.3363-24.031-81.5203-9.7163
230.5122-0.1750.31950.0596-0.11060.2071-0.1115-0.05670.10240.0534-0.0780.05430.0761-0.1463-0.32650.14370.01750.10320.4133-0.13870.2841-16.0422-82.1561-1.7002
240.0530.00260.02460.00980.00630.0348-0.0263-0.02950.0423-0.0096-0.04530.0218-0.0372-0.0531-0.12480.3041-0.1356-0.25320.29360.06640.5231-15.6544-81.3878-7.8904
250.0030.00330.00610.00230.00410.00690.04430.0214-0.01460.01420.07740.00730.03680.000300.991-0.1039-0.22060.5166-0.03630.6517-25.6374-63.2807-17.2843
260.0067-0.00550.00140.0054-0.00470.0061-0.0143-0.01780.0237-0.0008-0.0285-0.0366-0.00240.0238-01.242-0.0963-0.05680.87540.18790.8217-9.8912-53.0745-38.2326
270.0129-0.00940.01420.0033-0.0080.0143-0.0161-0.0092-0.0557-0.04690.02170.0181-0.0553-0.017-0.0281.10190.1833-0.59070.866-0.16360.7571-20.5758-60.9001-33.6352
280.00090.00080.00080.0022-0.0020.0035-0.0003-0.01590.0109-0.00880.0103-0.00450.0318-0.0107-00.8245-0.0038-0.15490.48540.20820.5534-18.1809-63.1271-17.7368
290.00720.0025-0.00370.00360.00340.00610.05970.12930.013-0.03860.05360.0077-0.0477-0.0448-0.00011.0159-0.208-0.10260.90810.19960.8775-14.153-58.7685-41.1597
300.0103-0.01040.010.0098-0.010.0094-0.044-0.06110.0378-0.0261-0.0491-0.0413-0.0676-0.0502-0.03620.9480.1997-0.12530.81870.15960.8206-24.1798-52.8331-35.8112
310.0032-0.00620.00060.00810.001-0.0005-0.0963-0.0142-0.0447-0.0332-0.1129-0.03790.1566-0.074700.3862-0.0323-0.07060.45830.09690.70769.1941-111.867344.1519
320.0279-0.02660.00520.08860.06410.07950.075-0.0344-0.0182-0.0637-0.07610.00420.0926-0.0099-0.07310.2971-0.01420.0140.36440.25060.39235.1566-101.389638.3451
330.0017-0.0002-0.00250.0010.00060.0026-0.06810.0296-0.06090.0036-0.0059-0.02160.0643-0.008400.9460.04530.23380.86170.31260.81315.3199-101.238333.2715
340.0048-0.00510.00280.0071-0.00490.00180.06610.0344-0.0223-0.02280.0627-0.02980.03860.0779-00.67540.0889-0.04140.48220.03590.85239.2227-110.313935.5899
350.0342-0.0832-0.10510.20590.25870.3271-0.0702-0.0115-0.02240.1569-0.2615-0.0685-0.04030.0641-0.13540.225-0.0204-0.09550.41420.21470.619711.7016-105.159245.8727
36-0.00060.0001-0.00050.0019-0.00270.0033-0.016-0.0092-0.0451-0.0296-0.015-0.04610.0168-0.010601.1443-0.0362-0.45610.6540.05380.6726.9111-95.959377.1556
370.061-0.01330.04590.04920.06190.14390.05410.01420.10570.04630.0033-0.0612-0.0147-0.03720.07150.746-0.0501-0.19860.48890.16650.82523.218-106.47668.1207
380.0054-0.0059-0.0040.01190.00110.0042-0.033-0.02460.04480.01220.02630.04550.0115-0.00560.02590.9781-0.2332-0.26040.6220.09190.603922.958-99.66283.0409
390.0206-0.01130.01230.0111-0.00920.00770.0177-0.01940.0348-0.0314-0.0512-0.00160.00160.07840.02560.8929-0.0437-0.49630.51780.07720.683631.9619-106.973777.7789
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 231 through 326 )
2X-RAY DIFFRACTION2chain 'A' and (resid 327 through 396 )
3X-RAY DIFFRACTION3chain 'A' and (resid 397 through 458 )
4X-RAY DIFFRACTION4chain 'A' and (resid 459 through 544 )
5X-RAY DIFFRACTION5chain 'B' and (resid 231 through 337 )
6X-RAY DIFFRACTION6chain 'B' and (resid 338 through 544 )
7X-RAY DIFFRACTION7chain 'I' and (resid 2 through 40 )
8X-RAY DIFFRACTION8chain 'I' and (resid 41 through 60 )
9X-RAY DIFFRACTION9chain 'I' and (resid 61 through 151 )
10X-RAY DIFFRACTION10chain 'I' and (resid 152 through 217 )
11X-RAY DIFFRACTION11chain 'H' and (resid 2 through 16 )
12X-RAY DIFFRACTION12chain 'H' and (resid 17 through 39 )
13X-RAY DIFFRACTION13chain 'H' and (resid 40 through 51 )
14X-RAY DIFFRACTION14chain 'H' and (resid 52 through 77 )
15X-RAY DIFFRACTION15chain 'H' and (resid 78 through 92 )
16X-RAY DIFFRACTION16chain 'H' and (resid 93 through 109 )
17X-RAY DIFFRACTION17chain 'H' and (resid 110 through 125 )
18X-RAY DIFFRACTION18chain 'H' and (resid 126 through 151 )
19X-RAY DIFFRACTION19chain 'H' and (resid 152 through 171 )
20X-RAY DIFFRACTION20chain 'H' and (resid 172 through 210 )
21X-RAY DIFFRACTION21chain 'H' and (resid 211 through 220 )
22X-RAY DIFFRACTION22chain 'M' and (resid 1 through 25 )
23X-RAY DIFFRACTION23chain 'M' and (resid 26 through 79 )
24X-RAY DIFFRACTION24chain 'M' and (resid 80 through 106 )
25X-RAY DIFFRACTION25chain 'M' and (resid 107 through 117 )
26X-RAY DIFFRACTION26chain 'M' and (resid 118 through 135 )
27X-RAY DIFFRACTION27chain 'M' and (resid 136 through 167 )
28X-RAY DIFFRACTION28chain 'M' and (resid 168 through 178 )
29X-RAY DIFFRACTION29chain 'M' and (resid 179 through 195 )
30X-RAY DIFFRACTION30chain 'M' and (resid 196 through 216 )
31X-RAY DIFFRACTION31chain 'L' and (resid 1 through 25 )
32X-RAY DIFFRACTION32chain 'L' and (resid 26 through 52 )
33X-RAY DIFFRACTION33chain 'L' and (resid 53 through 65 )
34X-RAY DIFFRACTION34chain 'L' and (resid 66 through 79 )
35X-RAY DIFFRACTION35chain 'L' and (resid 80 through 117 )
36X-RAY DIFFRACTION36chain 'L' and (resid 118 through 141 )
37X-RAY DIFFRACTION37chain 'L' and (resid 142 through 178 )
38X-RAY DIFFRACTION38chain 'L' and (resid 179 through 194 )
39X-RAY DIFFRACTION39chain 'L' and (resid 195 through 218 )

+
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