[English] 日本語
Yorodumi
- PDB-7shu: IgE-Fc in complex with omalizumab variant C02 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7shu
TitleIgE-Fc in complex with omalizumab variant C02
Components
  • (omalizumab variant C02 ...) x 2
  • Immunoglobulin heavy constant epsilon
KeywordsIMMUNE SYSTEM / IgE / omalizumab / xolair / inhibitor
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 / immunoglobulin complex, circulating / Role of LAT2/NTAL/LAB on calcium mobilization / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
PHOSPHATE ION / Immunoglobulin heavy constant epsilon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsPennington, L.F. / Jardetzky, T.J. / Kleinboelting, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI115469 United States
CitationJournal: Nat Commun / Year: 2021
Title: Directed evolution of and structural insights into antibody-mediated disruption of a stable receptor-ligand complex.
Authors: Luke F Pennington / Pascal Gasser / Silke Kleinboelting / Chensong Zhang / Georgios Skiniotis / Alexander Eggel / Theodore S Jardetzky /
Abstract: Antibody drugs exert therapeutic effects via a range of mechanisms, including competitive inhibition, allosteric modulation, and immune effector mechanisms. Facilitated dissociation is an additional ...Antibody drugs exert therapeutic effects via a range of mechanisms, including competitive inhibition, allosteric modulation, and immune effector mechanisms. Facilitated dissociation is an additional mechanism where antibody-mediated "disruption" of stable high-affinity macromolecular complexes can potentially enhance therapeutic efficacy. However, this mechanism is not well understood or utilized therapeutically. Here, we investigate and engineer the weak disruptive activity of an existing therapeutic antibody, omalizumab, which targets IgE antibodies to block the allergic response. We develop a yeast display approach to select for and engineer antibody disruptive efficiency and generate potent omalizumab variants that dissociate receptor-bound IgE. We determine a low resolution cryo-EM structure of a transient disruption intermediate containing the IgE-Fc, its partially dissociated receptor and an antibody inhibitor. Our results provide a conceptual framework for engineering disruptive inhibitors for other targets, insights into the failure in clinical trials of the previous high affinity omalizumab HAE variant and anti-IgE antibodies that safely and rapidly disarm allergic effector cells.
History
DepositionOct 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: omalizumab variant C02 VH
F: omalizumab variant C02 VL
B: Immunoglobulin heavy constant epsilon
C: omalizumab variant C02 VH
D: omalizumab variant C02 VL
A: Immunoglobulin heavy constant epsilon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,91911
Polymers105,2476
Non-polymers1,6725
Water23413
1
E: omalizumab variant C02 VH
F: omalizumab variant C02 VL
B: Immunoglobulin heavy constant epsilon
hetero molecules

B: Immunoglobulin heavy constant epsilon


Theoretical massNumber of molelcules
Total (without water)78,3178
Polymers77,1904
Non-polymers1,1274
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
2
C: omalizumab variant C02 VH
D: omalizumab variant C02 VL
A: Immunoglobulin heavy constant epsilon
hetero molecules

A: Immunoglobulin heavy constant epsilon


Theoretical massNumber of molelcules
Total (without water)77,7365
Polymers77,1904
Non-polymers5451
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)90.070, 176.120, 142.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-603-

HOH

21A-601-

HOH

-
Components

-
Protein , 1 types, 2 molecules BA

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


Mass: 24566.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHE / Production host: Homo sapiens (human) / References: UniProt: P01854

-
Antibody , 2 types, 4 molecules ECFD

#1: Antibody omalizumab variant C02 VH


Mass: 13437.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody omalizumab variant C02 VL


Mass: 14618.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Sugars , 3 types, 3 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 545.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4[DManpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{}[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#6: 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

-
Non-polymers , 3 types, 15 molecules

#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M Lithium sulfate, 0.1 M Phosphate citrate pH 4.2, 20% (w/v) PEG 1000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: PIXEL / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.75→49.1898 Å / Num. obs: 29871 / % possible obs: 99.85 % / Redundancy: 8.3 % / Biso Wilson estimate: 74.62 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.21
Reflection shellResolution: 2.75→2.848 Å / Mean I/σ(I) obs: 1.83 / Num. unique obs: 2928 / CC1/2: 0.676

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5hys

5hys


Resolution: 2.75→49.1898 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2746 1492 5 %
Rwork0.2198 28359 -
obs0.2226 29851 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 249.19 Å2 / Biso mean: 98.9123 Å2 / Biso min: 35.45 Å2
Refinement stepCycle: final / Resolution: 2.75→49.1898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6427 0 115 13 6555
Biso mean--123.53 67.4 -
Num. residues----838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036700
X-RAY DIFFRACTIONf_angle_d0.5489122
X-RAY DIFFRACTIONf_chiral_restr0.0391025
X-RAY DIFFRACTIONf_plane_restr0.0041159
X-RAY DIFFRACTIONf_dihedral_angle_d14.9993962
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7501-2.83890.37231330.335825462679100
2.8389-2.94030.4221330.303825272660100
2.9403-3.0580.35451340.29625402674100
3.058-3.19720.35661350.278925612696100
3.1972-3.36570.29091340.253825552689100
3.3657-3.57650.31651350.22925612696100
3.5765-3.85260.29361360.227125742710100
3.8526-4.24010.27221350.202125682703100
4.2401-4.85310.23261360.167925832719100
4.8531-6.11260.2321380.194826272765100
6.1126-49.18980.24741430.22352717286099
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)
14.03442.5266-1.1982.71580.24027.44520.36560.8086-0.5138-0.05850.1236-0.8238-0.23980.7561-0.49190.8510.08630.20790.6906-0.00250.7905-6.3994-36.94253.2699
28.5977-0.74883.74148.1992-5.74245.2723-0.2328-0.3664-0.1034-0.60610.11450.20340.4498-0.4616-0.14250.66530.02520.00550.5725-0.24730.6862-23.4268-44.70444.8613
33.03674.7824-2.04759.2318-2.67123.1102-0.2669-0.8485-0.3556-0.04290.5468-0.82330.01380.2801-0.17250.5913-0.0010.06340.5726-0.17450.5852-11.8846-28.99628.4841
45.25775.27315.37675.1785.35245.48470.5506-0.63491.33720.3831-0.59840.37070.1047-0.6139-0.52130.8727-0.15640.0860.655-0.00090.4688-17.4756-28.88494.2465
57.65137.22424.55637.21913.47484.1866-0.3548-0.3961-0.5244-0.846-0.0534-1.37460.15550.15480.35511.0548-0.191-0.0230.70120.12560.9269-23.6127-33.6761-2.2575
69.1337-0.18375.23623.04433.21966.6342-1.6431.70791.4333-2.605-0.2504-1.3564-1.36131.12251.76721.4237-0.17070.20940.66540.03070.9266-13.9521-22.4475-2.8963
72.9628-0.5709-1.71773.7669-4.10066.5540.56230.3129-0.833-0.4659-0.65830.85630.99310.7685-0.13541.0411-0.05420.15760.7569-0.1290.7237-13.008-38.0807-2.8307
83.8355-2.5918-1.26131.71330.81265.35970.4811-0.27471.0854-0.0601-0.068-0.0862-0.71440.9437-0.45710.6984-0.06640.10990.5114-0.0560.6273-12.2862-29.07996.0701
99.2979-5.48380.47354.3542-2.24914.64440.8634-0.8229-0.5152-0.8284-0.22040.5355-0.0414-0.263-0.50210.59020.0475-0.02050.5531-0.04880.5589-24.7018-32.52611.3432
102.72360.9352-0.06694.0878-4.05144.59790.754-1.4601-1.54390.2951-0.4832-0.94581.02922.49830.00370.684-0.0385-0.00450.8866-0.17680.8143-1.9861-31.36787.0368
117.7548-2.42666.31818.4407-2.76535.1408-0.56980.03850.48610.93030.12950.0331-1.7720.25720.31630.8565-0.02770.12650.491-0.06180.5537-17.7296-18.138524.1182
127.68070.89130.69817.75860.98464.7055-0.1296-0.2144-0.31030.3339-0.010.24760.15070.07830.16460.6305-0.04010.11160.4601-0.03820.4475-23.9069-28.08820.5573
134.57581.29422.62553.84992.08595.87780.063-0.1708-0.13140.16010.04340.4310.5297-0.0107-0.02270.7018-0.04620.08330.3050.01310.5097-18.4654-23.741921.6903
140.3012-0.46611.29113.08610.31032.98220.5876-0.32220.40490.6561-0.46461.0039-0.5085-0.3859-0.14990.7926-0.19720.17250.7565-0.01340.9543-45.8703-41.143215.2418
153.4844-2.25170.95523.9512-4.14165.30570.725-0.31390.94130.1046-0.6055-0.2849-0.0384-0.1637-0.14520.7144-0.13460.00710.538-0.14690.915-37.5462-42.280216.4412
167.30273.0564-0.18896.90760.78255.7001-0.2966-0.1202-0.2374-0.25310.17550.30730.3147-0.21030.14050.44790.0016-0.0790.4016-0.01270.4164-47.4095-68.150230.3263
177.11125.59163.77896.51432.20087.7874-0.4034-0.1880.189-0.26190.38110.294-0.28090.47450.03430.4285-0.0153-0.13540.59790.03380.7104-45.6619-61.551527.2035
186.19324.7886-3.46084.3027-2.37534.0526-0.77920.4239-0.0698-0.57360.4825-0.03060.5281-0.32020.26980.4729-0.0776-0.13560.4359-0.01320.529-47.1531-69.915524.4593
198.5044.3995-1.52047.5962-2.00416.84710.316-0.07960.2098-0.01710.04950.87750.472-1.357-0.44950.8512-0.1038-0.15960.64330.09810.6738-47.3541-83.536116.3069
205.94763.4582-1.82866.8609-1.57975.25650.03350.20650.0178-0.4155-0.2551-0.08430.31410.142-0.02350.7976-0.0688-0.04710.67710.10290.3678-35.7582-81.311913.9162
218.1761-2.94652.0782.590.63845.3086-0.3790.0935-1.7892-1.03810.4210.53251.9197-0.5187-0.55711.2456-0.0379-0.21660.7076-0.03050.7163-39.2384-93.719518.3406
227.84935.2923-0.01123.96-2.06949.1332-1.04480.4016-0.2443-2.29120.0978-0.38650.88740.73350.83071.27660.00220.04440.8348-0.08750.5834-33.2477-90.21476.7254
235.75525.1653-1.76124.5904-1.87163.2455-0.79610.96660.5054-1.040.93221.08670.76680.1205-0.22141.1642-0.285-0.12420.8680.09440.6418-40.8562-83.19947.6752
247.96060.2825-0.33955.3133-1.22762.51691.1970.4448-0.7724-0.8121-0.4661-0.1111.60221.1493-0.3191.5055-0.3235-0.14270.9068-0.03870.8309-50.6586-95.728412.867
252.1843-0.85771.68655.07710.11924.60121.58580.5910.4652-0.6026-1.0848-0.75621.04170.2094-0.07440.8127-0.01340.0470.72550.13490.5314-32.9321-86.726518.5041
265.84332.57912.73365.6909-1.71393.1683-1.1451-0.2149-1.3438-0.31050.0671-0.97882.02631.73851.27111.18140.33280.25860.73670.14680.618-25.827-88.246717.8481
279.1668-0.13443.02175.52633.2162.83430.0151-0.15381.63390.65010.12952.11881.162-1.4230.14810.9568-0.23790.03810.91830.18750.5144-50.6184-88.534520.0626
286.6544-0.2814-5.11056.37290.81693.9531-0.44860.7994-0.4576-1.87550.13510.55641.625-1.52840.92291.7189-0.03190.06290.7887-0.08250.7982-32.0915-105.166823.0302
292.39711.2032-3.19436.76350.76736.3445-0.0593-1.3051-0.50521.0011-0.93140.4394-0.534-0.27440.57221.02480.2785-0.26820.55060.08640.5186-30.1062-98.443244.5397
303.6760.2212-2.20952.72270.85041.84280.20840.5969-0.5456-1.3067-0.1236-0.13392.0658-0.27520.86851.12980.41350.20890.4778-0.07070.7041-26.5684-103.432432.4274
319.31810.08720.35485.6616-2.69025.4079-0.60870.1209-1.0391-0.91350.0826-0.82071.44520.81390.690.98540.20020.27840.80690.04010.6707-23.148-98.159321.6834
321.36360.38871.21526.8027-4.2554.2745-0.7276-1.19770.27621.95770.47060.9428-0.65960.74030.19560.72580.23880.05470.8587-0.0410.647-33.2014-87.585130.4661
338.043-2.1418-1.52356.34991.97888.8396-0.28730.1422-0.37330.3721-0.7042-1.06280.13491.94430.48960.61370.15460.02420.84230.14660.7259-20.1552-90.868430.4125
342.02370.011-6.3817.46970.96287.5985-1.29071.3778-1.9506-0.53580.0725-1.71012.71421.55680.05360.70.41560.09810.887-0.04190.8663-22.3646-101.370730.3408
359.28970.59392.31961.976-0.03722.57580.7542-0.7243-0.18870.35990.2745-0.8489-1.62950.3097-0.16490.76020.1173-0.04450.6036-0.07660.7343-29.5194-90.67742.1655
365.0874-1.21830.71673.76470.43191.73170.37811.09030.0445-1.35720.0895-0.69041.16080.3312-0.31111.35970.07750.14260.6705-0.06110.5333-30.6225-97.951121.7403
372.9515-3.6809-3.08295.46043.99453.56390.1132-0.81890.4789-0.70220.19141.11571.9352-2.4825-0.16880.72820.00590.17820.96850.15490.6861-38.0117-97.728343.1401
387.0733-6.0375-0.00375.9313-0.1315-0.01670.09030.49420.3858-1.6433-0.7146-1.32770.25330.54920.84490.7428-0.04830.02351.44430.27061.1449-5.3041-75.606115.6524
391.73642.5841.76782.75241.57284.3577-0.11770.26340.0938-0.5399-0.4678-0.801-0.9721-0.44380.50251.00760.0039-0.03641.12770.35721.3643-7.9555-69.00121.7204
402.35040.2029-0.20950.81161.65292.82410.38320.696-0.6752-0.3001-0.5203-0.724-0.83110.49860.33521.35280.072-0.35531.29210.30761.8147-0.4371-52.328523.7543
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 1 through 25 )E1 - 25
2X-RAY DIFFRACTION2chain 'E' and (resid 26 through 33 )E26 - 33
3X-RAY DIFFRACTION3chain 'E' and (resid 34 through 45 )E34 - 45
4X-RAY DIFFRACTION4chain 'E' and (resid 46 through 53 )E46 - 53
5X-RAY DIFFRACTION5chain 'E' and (resid 54 through 60 )E54 - 60
6X-RAY DIFFRACTION6chain 'E' and (resid 61 through 67 )E61 - 67
7X-RAY DIFFRACTION7chain 'E' and (resid 68 through 84 )E68 - 84
8X-RAY DIFFRACTION8chain 'E' and (resid 85 through 102 )E85 - 102
9X-RAY DIFFRACTION9chain 'E' and (resid 103 through 111 )E103 - 111
10X-RAY DIFFRACTION10chain 'E' and (resid 112 through 120 )E112 - 120
11X-RAY DIFFRACTION11chain 'F' and (resid -1 through 25 )F-1 - 25
12X-RAY DIFFRACTION12chain 'F' and (resid 26 through 71 )F26 - 71
13X-RAY DIFFRACTION13chain 'F' and (resid 72 through 110 )F72 - 110
14X-RAY DIFFRACTION14chain 'B' and (resid 336 through 397 )B336 - 397
15X-RAY DIFFRACTION15chain 'B' and (resid 398 through 443 )B398 - 443
16X-RAY DIFFRACTION16chain 'B' and (resid 444 through 480 )B444 - 480
17X-RAY DIFFRACTION17chain 'B' and (resid 481 through 502 )B481 - 502
18X-RAY DIFFRACTION18chain 'B' and (resid 503 through 544 )B503 - 544
19X-RAY DIFFRACTION19chain 'C' and (resid 1 through 17 )C1 - 17
20X-RAY DIFFRACTION20chain 'C' and (resid 18 through 40 )C18 - 40
21X-RAY DIFFRACTION21chain 'C' and (resid 41 through 52 )C41 - 52
22X-RAY DIFFRACTION22chain 'C' and (resid 53 through 64 )C53 - 64
23X-RAY DIFFRACTION23chain 'C' and (resid 65 through 83 )C65 - 83
24X-RAY DIFFRACTION24chain 'C' and (resid 84 through 91 )C84 - 91
25X-RAY DIFFRACTION25chain 'C' and (resid 92 through 102 )C92 - 102
26X-RAY DIFFRACTION26chain 'C' and (resid 103 through 111 )C103 - 111
27X-RAY DIFFRACTION27chain 'C' and (resid 112 through 122 )C112 - 122
28X-RAY DIFFRACTION28chain 'D' and (resid -1 through 9 )D-1 - 9
29X-RAY DIFFRACTION29chain 'D' and (resid 10 through 18 )D10 - 18
30X-RAY DIFFRACTION30chain 'D' and (resid 19 through 24 )D19 - 24
31X-RAY DIFFRACTION31chain 'D' and (resid 25 through 42 )D25 - 42
32X-RAY DIFFRACTION32chain 'D' and (resid 43 through 52 )D43 - 52
33X-RAY DIFFRACTION33chain 'D' and (resid 53 through 71 )D53 - 71
34X-RAY DIFFRACTION34chain 'D' and (resid 72 through 79 )D72 - 79
35X-RAY DIFFRACTION35chain 'D' and (resid 80 through 88 )D80 - 88
36X-RAY DIFFRACTION36chain 'D' and (resid 89 through 106 )D89 - 106
37X-RAY DIFFRACTION37chain 'D' and (resid 107 through 113 )D107 - 113
38X-RAY DIFFRACTION38chain 'A' and (resid 339 through 372 )A339 - 372
39X-RAY DIFFRACTION39chain 'A' and (resid 373 through 502 )A373 - 502
40X-RAY DIFFRACTION40chain 'A' and (resid 503 through 541 )A503 - 541

+
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