[English] 日本語
Yorodumi
- PDB-5jw4: Structure of MEDI8852 Fab Fragment in Complex with H5 HA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jw4
TitleStructure of MEDI8852 Fab Fragment in Complex with H5 HA
Components
  • (Hemagglutinin) x 2
  • (MEDI8852 heavy ...) x 2
  • (MEDI8852 light ...) x 2
KeywordsIMMUNE SYSTEM / Antibody Influenza Broadly Neutralizing
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsNeu, U. / Collins, P.J. / Walker, P.A. / Vorlaender, M.K. / Ogrodowicz, R.W. / Martin, S.R. / Gamblin, S.J. / Skehel, J.J.
CitationJournal: Cell / Year: 2016
Title: Structure and Function Analysis of an Antibody Recognizing All Influenza A Subtypes.
Authors: Kallewaard, N.L. / Corti, D. / Collins, P.J. / Neu, U. / McAuliffe, J.M. / Benjamin, E. / Wachter-Rosati, L. / Palmer-Hill, F.J. / Yuan, A.Q. / Walker, P.A. / Vorlaender, M.K. / Bianchi, S. ...Authors: Kallewaard, N.L. / Corti, D. / Collins, P.J. / Neu, U. / McAuliffe, J.M. / Benjamin, E. / Wachter-Rosati, L. / Palmer-Hill, F.J. / Yuan, A.Q. / Walker, P.A. / Vorlaender, M.K. / Bianchi, S. / Guarino, B. / De Marco, A. / Vanzetta, F. / Agatic, G. / Foglierini, M. / Pinna, D. / Fernandez-Rodriguez, B. / Fruehwirth, A. / Silacci, C. / Ogrodowicz, R.W. / Martin, S.R. / Sallusto, F. / Suzich, J.A. / Lanzavecchia, A. / Zhu, Q. / Gamblin, S.J. / Skehel, J.J.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Nov 21, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / entity_src_nat / pdbx_validate_polymer_linkage / struct_ref / struct_ref_seq
Item: _entity.pdbx_mutation / _entity.src_method ..._entity.pdbx_mutation / _entity.src_method / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1 / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.3Apr 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / pdbx_validate_close_contact / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
G: Hemagglutinin
H: Hemagglutinin
I: Hemagglutinin
J: Hemagglutinin
K: Hemagglutinin
L: Hemagglutinin
M: MEDI8852 heavy chain
N: MEDI8852 light chain
O: MEDI8852 heavy chain
P: MEDI8852 light chain
Q: MEDI8852 heavy chain
R: MEDI8852 light chain
S: MEDI8852 heavy chain
T: MEDI8852 light chain
U: MEDI8852 heavy chain
V: MEDI8852 light chain
W: MEDI8852 heavy chain
X: MEDI8852 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)618,41549
Polymers611,86824
Non-polymers6,54625
Water00
1
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
M: MEDI8852 heavy chain
N: MEDI8852 light chain
O: MEDI8852 heavy chain
P: MEDI8852 light chain
Q: MEDI8852 heavy chain
R: MEDI8852 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,61624
Polymers306,35212
Non-polymers3,26412
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
G: Hemagglutinin
H: Hemagglutinin
I: Hemagglutinin
J: Hemagglutinin
K: Hemagglutinin
L: Hemagglutinin
S: MEDI8852 heavy chain
T: MEDI8852 light chain
U: MEDI8852 heavy chain
V: MEDI8852 light chain
W: MEDI8852 heavy chain
X: MEDI8852 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)308,79825
Polymers305,51612
Non-polymers3,28213
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)151.260, 386.360, 165.860
Angle α, β, γ (deg.)90.000, 90.440, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein
Hemagglutinin


Mass: 36293.109 Da / Num. of mol.: 6 / Mutation: K198N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Gallus gallus (chicken) / References: UniProt: Q6DQ34
#2: Protein
Hemagglutinin


Mass: 18681.605 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: HA / Production host: Gallus gallus (chicken) / References: UniProt: Q6DQ34, UniProt: Q6DQ18*PLUS

-
Antibody , 4 types, 12 molecules MOSUWNPTVXQR

#3: Antibody
MEDI8852 heavy chain


Mass: 24413.189 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#4: Antibody
MEDI8852 light chain


Mass: 22450.832 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#5: Antibody MEDI8852 heavy chain


Mass: 24789.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#6: Antibody MEDI8852 light chain


Mass: 22910.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)

-
Sugars , 2 types, 25 molecules

#7: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#8: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 20
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: 3.96 Å3/Da / Density % sol: 68.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 16% PEG3350, 0.1 M PIPES pH 7.0, cryoprotected with 25% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.7→29.796 Å / Num. obs: 98353 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 2.18 % / Biso Wilson estimate: 136.3 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.123 / Net I/σ(I): 7.05
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.7-3.80.9120.99198.3
3.8-3.90.7681.23198.3
3.9-4.010.621.57198.4
4.01-4.140.5021.94197.7
4.14-4.270.3742.55198.2
4.27-4.420.2773.55198
4.42-4.590.2124.41198
4.59-4.780.1965.06198.3
4.78-4.990.1745.53197.9
4.99-5.230.156.13197.9
5.23-5.520.1336.94198
5.52-5.850.1267.13198
5.85-6.250.1088.03198.6
6.25-6.760.0929.3197.8
6.76-7.40.06911.52198
7.4-8.270.04417.31196.1
8.27-9.550.03124.23193.5
9.55-11.70.02329.89194.9
11.7-16.550.0232.07194.3
16.550.01936.27174.5

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BGW and 5JW5

4bgw

5jw5


Resolution: 3.7→29.796 Å / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.62
RfactorNum. reflection% reflection
Rfree0.2851 4768 4.85 %
Rwork0.2736 --
obs0.2741 98333 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 268.13 Å2 / Biso mean: 152.8518 Å2 / Biso min: 99.46 Å2
Refinement stepCycle: final / Resolution: 3.7→29.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41993 0 420 0 42413
Biso mean--155.41 --
Num. residues----5368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01843499
X-RAY DIFFRACTIONf_angle_d1.4758971
X-RAY DIFFRACTIONf_chiral_restr0.076524
X-RAY DIFFRACTIONf_plane_restr0.0087590
X-RAY DIFFRACTIONf_dihedral_angle_d14.01615767
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6999-3.74190.37011540.40363103325798
3.7419-3.78590.36641420.38293187332998
3.7859-3.83190.40031680.37373089325798
3.8319-3.88030.38621210.36373181330299
3.8803-3.93130.31361540.36783135328998
3.9313-3.9850.34531420.35353162330499
3.985-4.04180.35491880.35013081326998
4.0418-4.1020.37341420.35443128327097
4.102-4.16590.36321770.35033130330798
4.1659-4.2340.33691540.33163152330698
4.234-4.30680.341670.31973121328898
4.3068-4.38490.3021530.3083132328598
4.3849-4.4690.32061900.29273091328198
4.469-4.55990.29851650.28983112327798
4.5599-4.65870.29291720.28433148332098
4.6587-4.76660.2941500.28043111326198
4.7666-4.88530.30641750.27523127330298
4.8853-5.01680.27171780.28293113329198
5.0168-5.16370.25981430.27383129327298
5.1637-5.32950.29011830.26873109329298
5.3295-5.51880.28911610.26133158331998
5.5188-5.73820.29971730.26513094326798
5.7382-5.99740.27551620.2733134329699
5.9974-6.31080.26961640.26463164332898
6.3108-6.70190.29811400.26573118325898
6.7019-7.21260.28111740.26863160333498
7.2126-7.9260.26131590.2493084324397
7.926-9.04480.21341540.20253011316594
9.0448-11.29140.20691310.18943054318594
11.2914-29.79680.24031320.24583047317993
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)
11.40871.24582.99631.5289-0.07792.75710.1818-0.1374-0.50380.518-0.1363-0.30530.49790.1021-01.7032-0.1498-0.12011.30140.02561.413748.797646.080147.1352
21.15950.3034-2.41190.76120.0641.07190.1917-0.2617-0.68930.2278-0.04660.06320.10970.2458-02.05720.1519-0.51491.4507-0.12342.563581.186134.054249.97
33.12311.1611-1.03041.99971.78260.75920.4652-0.4012-1.8172-0.009-0.2161-1.05640.48430.711601.92330.3488-0.34981.9695-0.04722.889101.318832.573150.5838
41.0741.30451.57860.6508-0.10292.99290.01780.3277-0.46710.0780.00310.02120.1403-0.26920.01661.3863-0.0809-0.05351.2433-0.271.534234.313356.556335.143
51.9478-2.47962.01422.7679-0.86271.3315-0.05510.8107-0.5328-0.027-0.0062-0.2387-0.10850.4539-01.4323-0.138-0.02521.5399-0.2081.004860.156964.306617.2051
61.92291.19032.22030.8535-1.81431.97530.07580.8543-0.1814-0.48530.2970.05640.71710.777801.5259-0.0632-0.05342.31640.00531.625394.145662.713923.6638
74.35052.3339-1.63190.83320.10064.6091-0.08370.7523-0.5989-0.11460.5141-0.50620.55541.7825-01.61850.2302-0.29662.5816-0.31541.8185112.130159.74432.3286
80.8425-1.88020.77552.0533-0.33371.8091-0.17560.51380.03540.1119-0.0710.0062-0.2622-0.0428-0.01331.4706-0.0413-0.08381.2936-0.00381.244841.241371.943822.5069
95.3240.8115-1.61421.10090.553-0.0939-0.3212-0.37630.40780.15230.1842-0.5135-0.45870.2838-01.771-0.0683-0.22741.1317-0.16871.025956.930281.760849.2122
102.3349-0.36171.0610.2279-1.23911.47480.1831-0.7440.09020.2967-0.0843-0.0284-0.0801-0.1025-01.8437-0.0817-0.29451.7806-0.09921.508887.584272.166962.4774
114.5859-0.29582.11630.6868-0.09044.1240.0547-0.4101-0.0188-0.00430.2734-0.29930.15250.34-01.8399-0.063-0.27951.70430.04111.4709105.399663.130665.4858
122.3446-1.23-0.74841.42290.00371.1232-0.0519-0.1055-0.65210.1320.01940.289-0.1579-0.2526-0.0031.690.0405-0.12341.1981-0.10691.17337.032576.211942.9654
133.6099-0.83691.50461.524-0.3255-0.4222-0.4004-0.7956-0.03270.56720.07740.78980.5183-0.120201.7249-0.28420.36111.29910.04672.048198.4544-60.414148.8936
140.1879-0.605-0.36810.40061.23321.4778-0.0889-0.79920.44640.13380.12670.0256-0.0198-0.4009-01.9693-0.32110.67352.3226-0.17272.721369.035-50.143364.0505
15-0.2947-0.9442-0.40580.8724-1.3670.8111-0.3254-0.65890.77380.26610.25921.1379-0.0869-0.624-02.0916-0.34320.74652.6955-0.4783.611951.328-41.160367.6685
163.05751.88971.47590.4325-0.45261.4249-0.1274-0.2791.2990.15560.0071-0.247-0.0040.16030.00131.6324-0.11380.12741.30070.07871.3837117.4161-55.291240.4182
170.9658-0.2946-2.29170.06570.85583.0583-0.1051-0.00940.75410.2788-0.17410.2156-0.4509-0.278201.6663-0.20650.11721.37910.07152.2729105.4719-24.93542.7584
181.1618-0.1590.98470.73980.135-0.25350.0469-0.45531.19990.2585-0.5004-0.05970.1148-0.494202.06050.24650.1061.7597-0.09573.969473.0889-13.284247.122
190.24571.61250.34851.1380.16770.53450.1722-0.24750.42190.2418-0.00930.24780.1971-0.944602.13990.48180.21172.5828-0.21274.071153.0347-12.343649.3873
201.57870.8019-2.54391.25210.32263.4692-0.4170.6323-0.19460.1802-0.00590.08530.0211-0.07450.01651.3525-0.1190.19371.26220.35472.1551119.2373-36.253630.6415
211.2379-0.2307-1.60452.07810.60021.618-0.37110.71790.8879-0.05540.12530.84220.3725-0.394301.4134-0.1587-0.01311.51940.37622.04992.0542-45.83815.5828
220.6349-0.424-1.18440.9652-0.48490.94240.16920.09951.098-0.395-0.05250.3016-0.4576-0.457101.374-0.3066-0.03642.14370.02493.630658.6807-44.534424.7066
232.3994-0.053-0.35032.4204-0.51283.57580.2337-0.05410.302-0.1154-0.11820.1982-0.5484-1.410101.5447-0.11760.19442.22980.01133.686141.4027-41.378634.6279
242.7559-0.8089-0.31421.37210.79622.0899-0.10290.22450.1845-0.07850.03510.42410.16620.2608-0.01491.5079-0.10930.17951.24970.25851.856111.4004-52.707619.973
252.25571.4497-2.57564.69550.44811.95950.1686-0.5313-0.28370.5424-0.37530.16890.3647-0.589301.3653-0.21640.04481.4519-0.1131.383717.109529.585136.963
262.04930.35630.82491.41990.27522.87760.2554-0.89810.11920.89190.1554-0.45531.0384-0.3181-01.8303-0.3280.0211.67440.0721.690121.9067-1.640928.8405
271.6410.817-0.32572.1834-2.61376.11460.4460.9464-0.6068-0.3539-0.58480.00080.06230.3454-01.40840.1602-0.10291.7355-0.16761.048840.376582.8911-8.0379
281.0031-0.14880.37681.5665-0.19160.64350.71160.8936-0.4094-0.6564-0.3153-1.13190.24580.394601.84410.39330.18622.38930.1371.466560.319199.731-26.6467
292.4103-1.6971-0.87263.71071.66723.29320.2764-0.14130.5003-0.066-0.1986-0.0347-0.622-0.347401.70460.11770.08541.17280.01641.15126.731399.522562.764
304.3201-0.9168-1.24744.2976-1.6752.96020.0533-0.9044-0.07030.2075-0.5981-0.28920.03871.1054-01.6990.0030.10661.56590.04861.2789129.7194-76.760961.2715
31-0.2331-1.4477-0.01280.4668-0.32250.5235-0.0847-0.8797-0.27240.52420.15820.64740.43081.638102.0276-0.15110.05973.2630.46262.1522128.7067-82.178593.2304
323.62510.65641.50992.7864-0.81991.87720.3797-0.6251-0.17360.4221-0.1147-0.2312-0.30840.094201.4091-0.28150.01711.33060.17631.7019136.5194-9.212729.6983
331.87050.1319-1.26431.27960.76871.4129-0.2368-0.6790.19090.3833-0.0372-0.1412-1.1615-0.0489-02.1916-0.0484-0.02981.4375-0.01171.6975130.969121.528921.0979
340.53083.43531.34262.09322.2473.82360.13460.72280.5972-0.3031-0.3019-0.0204-0.4152-0.035701.39430.26770.06691.74260.36731.4667109.1641-66.501-9.4933
350.2996-0.0264-0.30390.8041-0.10161.08750.29410.89740.2132-0.0708-0.55310.79580.5123-0.582701.73110.3022-0.1292.51080.03921.747287.2049-84.9999-23.6711
364.21810.9368-1.94042.31392.51825.3303-0.1757-0.0509-0.0852-0.24040.3215-0.098-0.27090.074601.2343-0.23120.00981.2085-0.10451.459634.547429.252321.6474
372.3581-1.3985-3.28662.17830.36682.6312-0.10670.2969-0.3994-0.0467-0.008-0.00240.5936-0.487701.6982-0.2528-0.13531.173-0.01131.901922.9002-4.306512.4625
381.10181.91150.34162.4584-1.06951.71840.13540.21780.81520.3732-0.4626-0.2406-0.81190.705-01.7302-0.1502-0.17021.89710.10991.086353.899394.89796.4633
392.34170.8112-0.12893.341.47642.20050.3280.51830.2783-0.0803-0.4599-0.617-0.6548-0.015901.6633-0.03620.10982.5340.4761.598162.2453115.7374-22.9501
402.6583-1.8239-3.64532.01450.06922.4625-0.1118-0.7773-0.970.6557-0.01510.19820.4696-0.0809-01.8434-0.005-0.18461.39780.21651.203732.942879.849873.1979
410.4913-1.46591.75571.27850.23132.2934-0.3275-0.79840.67580.45430.3165-0.3682-1.09330.5893-02.4578-0.4310.34031.808-0.33641.5662124.2734-56.388970.7401
421.0511-0.00460.86131.02560.03860.7157-0.4545-0.662-0.00320.6179-0.183-0.19170.02150.762902.3422-0.3417-0.00313.8540.16781.7837136.3657-71.2605102.792
432.4347-0.28451.2051.2258-2.86253.4563-0.33790.1888-0.0458-0.49470.28210.2874-0.18260.012-01.4752-0.2349-0.05821.23650.12741.8136118.0853-9.63615.4889
442.864-1.49331.9260.881.25890.055-0.39090.01370.3028-0.17830.0378-0.3094-0.45290.2267-02.0294-0.06430.00471.34860.02451.6058128.804823.87424.9406
450.7785-0.6128-0.68934.0860.78582.9630.1607-0.04390.00990.428-0.4296-0.12880.3817-0.8269-01.5325-0.26570.08441.92430.20531.269797.7781-77.27527.6289
462.17041.7901-0.5672.13860.46430.69090.43360.5849-0.2106-0.1966-0.55360.56230.4671-0.175201.7492-0.0012-0.19872.4301-0.15881.698186.0042-100.7205-18.5487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resseq 1:46 or resseq 266:321)A1 - 46
2X-RAY DIFFRACTION1chain A and (resseq 1:46 or resseq 266:321)A266 - 321
3X-RAY DIFFRACTION2chain A and (resseq 47:111 or resseq 256:265)A47 - 111
4X-RAY DIFFRACTION2chain A and (resseq 47:111 or resseq 256:265)A256 - 265
5X-RAY DIFFRACTION3chain A and (resseq 112:255)A112 - 255
6X-RAY DIFFRACTION4chain BB1 - 162
7X-RAY DIFFRACTION5chain C and (resseq 1:46 or resseq 266:321)C1 - 46
8X-RAY DIFFRACTION5chain C and (resseq 1:46 or resseq 266:321)C266 - 321
9X-RAY DIFFRACTION6chain C and (resseq 47:111 or resseq 256:265)C47 - 111
10X-RAY DIFFRACTION6chain C and (resseq 47:111 or resseq 256:265)C256 - 265
11X-RAY DIFFRACTION7chain C and (resseq 112:255)C112 - 255
12X-RAY DIFFRACTION8chain DD1 - 162
13X-RAY DIFFRACTION9chain E and (resseq 1:46 or resseq 266:321)E1 - 46
14X-RAY DIFFRACTION9chain E and (resseq 1:46 or resseq 266:321)E266 - 321
15X-RAY DIFFRACTION10chain E and (resseq 47:111 or resseq 256:265)E47 - 111
16X-RAY DIFFRACTION10chain E and (resseq 47:111 or resseq 256:265)E256 - 265
17X-RAY DIFFRACTION11chain E and (resseq 112:255)E112 - 255
18X-RAY DIFFRACTION12chain FF1 - 162
19X-RAY DIFFRACTION13chain G and (resseq 1:46 or resseq 266:321)G1 - 46
20X-RAY DIFFRACTION13chain G and (resseq 1:46 or resseq 266:321)G266 - 321
21X-RAY DIFFRACTION14chain G and (resseq 47:111 or resseq 256:265)G47 - 111
22X-RAY DIFFRACTION14chain G and (resseq 47:111 or resseq 256:265)G256 - 265
23X-RAY DIFFRACTION15chain G and (resseq 112:255)G112 - 255
24X-RAY DIFFRACTION16chain HH1 - 162
25X-RAY DIFFRACTION17chain I and (resseq 1:46 or resseq 266:321)I1 - 46
26X-RAY DIFFRACTION17chain I and (resseq 1:46 or resseq 266:321)I266 - 321
27X-RAY DIFFRACTION18chain I and (resseq 47:111 or resseq 256:265)I47 - 111
28X-RAY DIFFRACTION18chain I and (resseq 47:111 or resseq 256:265)I256 - 265
29X-RAY DIFFRACTION19chain I and (resseq 112:255)I112 - 255
30X-RAY DIFFRACTION20chain JJ1 - 162
31X-RAY DIFFRACTION21chain K and (resseq 1:46 or resseq 266:321)K1 - 46
32X-RAY DIFFRACTION21chain K and (resseq 1:46 or resseq 266:321)K266 - 321
33X-RAY DIFFRACTION22chain K and (resseq 47:111 or resseq 256:265)K47 - 111
34X-RAY DIFFRACTION22chain K and (resseq 47:111 or resseq 256:265)K256 - 265
35X-RAY DIFFRACTION23chain K and (resseq 112:255)K112 - 255
36X-RAY DIFFRACTION24chain LL1 - 162
37X-RAY DIFFRACTION25chain M and resseq 1:128M1 - 128
38X-RAY DIFFRACTION26chain M and resseq 129:229M129 - 229
39X-RAY DIFFRACTION27chain O and resseq 1:128O1 - 128
40X-RAY DIFFRACTION28chain O and resseq 129:229O129 - 229
41X-RAY DIFFRACTION29chain Q and resseq 1:128Q1 - 128
42X-RAY DIFFRACTION30chain S and resseq 1:128S1 - 128
43X-RAY DIFFRACTION31chain S and resseq 129:229S129 - 229
44X-RAY DIFFRACTION32chain U and resseq 1:128U1 - 128
45X-RAY DIFFRACTION33chain U and resseq 129:229U129 - 229
46X-RAY DIFFRACTION34chain W and resseq 1:128W1 - 128
47X-RAY DIFFRACTION35chain W and resseq 129:229W129 - 229
48X-RAY DIFFRACTION36chain N and resseq 1:104N1 - 104
49X-RAY DIFFRACTION37chain N and resseq 105:210N105 - 210
50X-RAY DIFFRACTION38chain P and resseq 1:104P1 - 104
51X-RAY DIFFRACTION39chain P and resseq 105:210P105 - 210
52X-RAY DIFFRACTION40chain R and resseq 1:104R1 - 104
53X-RAY DIFFRACTION41chain T and resseq 1:104T1 - 104
54X-RAY DIFFRACTION42chain T and resseq 105:210T105 - 210
55X-RAY DIFFRACTION43chain V and resseq 1:104V1 - 104
56X-RAY DIFFRACTION44chain V and resseq 105:210V105 - 210
57X-RAY DIFFRACTION45chain X and resseq 1:104X1 - 104
58X-RAY DIFFRACTION46chain X and resseq 105:210X105 - 210

+
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://pdbjlvh1.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