[English] 日本語
Yorodumi
- PDB-6e56: Human antibody H2214 in complex with influenza hemagglutinin A/Ai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6.0E+56
TitleHuman antibody H2214 in complex with influenza hemagglutinin A/Aichi/2/1968 (X-31) (H3N2)
Components
  • (antibody H2214 ...) x 2
  • Hemagglutinin
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / influenza antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 / extracellular region / membrane
Similarity search - Function
Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 ...Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ribbon / Immunoglobulin subtype / Immunoglobulin / 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 / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Hemagglutinin / IGK@ protein
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMcCarthy, K.R. / Harrison, S.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI089618 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1U19AI117892-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI128832 United States
CitationJournal: Cell / Year: 2019
Title: Antibodies to a Conserved Influenza Head Interface Epitope Protect by an IgG Subtype-Dependent Mechanism.
Authors: Watanabe, A. / McCarthy, K.R. / Kuraoka, M. / Schmidt, A.G. / Adachi, Y. / Onodera, T. / Tonouchi, K. / Caradonna, T.M. / Bajic, G. / Song, S. / McGee, C.E. / Sempowski, G.D. / Feng, F. / ...Authors: Watanabe, A. / McCarthy, K.R. / Kuraoka, M. / Schmidt, A.G. / Adachi, Y. / Onodera, T. / Tonouchi, K. / Caradonna, T.M. / Bajic, G. / Song, S. / McGee, C.E. / Sempowski, G.D. / Feng, F. / Urick, P. / Kepler, T.B. / Takahashi, Y. / Harrison, S.C. / Kelsoe, G.
History
DepositionJul 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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.auth_asym_id / _atom_site.auth_seq_id ..._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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_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 2.1Oct 11, 2023Group: 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
D: Hemagglutinin
A: Hemagglutinin
H: antibody H2214 heavy chain
G: antibody H2214 heavy chain
I: antibody H2214 light chain, K1642
J: antibody H2214 light chain, K1642
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,03911
Polymers165,0546
Non-polymers9855
Water16,015889
1
D: Hemagglutinin
G: antibody H2214 heavy chain
I: antibody H2214 light chain, K1642
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2326
Polymers82,5273
Non-polymers7053
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hemagglutinin
H: antibody H2214 heavy chain
J: antibody H2214 light chain, K1642
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8075
Polymers82,5273
Non-polymers2802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.550, 98.710, 224.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

-
Protein , 1 types, 2 molecules DA

#1: Protein Hemagglutinin


Mass: 31993.994 Da / Num. of mol.: 2 / Fragment: head domain (UNP residues 53-335)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Aichi/2/1968 H3N2 / Gene: HA / Plasmid: pFB / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03437

-
Antibody , 2 types, 4 molecules HGIJ

#2: Antibody antibody H2214 heavy chain


Mass: 26955.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHV3-23*01 / Plasmid: pVRC / Cell line (production host): 293F / Production host: Homo sapiens (human)
#3: Antibody antibody H2214 light chain, K1642


Mass: 23577.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGKV3-15*01 / Plasmid: pVRC / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: Q6PIL8

-
Sugars , 2 types, 3 molecules

#4: 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.: 1
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)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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.: 2
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 , 2 types, 891 molecules

#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 889 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM sodium chloride, 100 mM sodium acetate, pH 5.0, 20% w/v PEG2000 MME

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2018
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→48.851 Å / Num. obs: 117279 / % possible obs: 99.38 % / Redundancy: 5.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1061 / Net I/σ(I): 10.67
Reflection shellResolution: 2→2.072 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.1214 / Mean I/σ(I) obs: 1.45 / Num. unique obs: 66956 / CC1/2: 0.544 / % possible all: 99.92

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 6B0A, 4FP8, 5Y11, 4YK4
Resolution: 2→48.851 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.34
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 5842 5.01 %random selection
Rwork0.1876 ---
obs0.189 116544 99.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→48.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11001 0 0 889 11890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411282
X-RAY DIFFRACTIONf_angle_d0.65215367
X-RAY DIFFRACTIONf_dihedral_angle_d3.5656683
X-RAY DIFFRACTIONf_chiral_restr0.0471719
X-RAY DIFFRACTIONf_plane_restr0.0051977
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.30411910.29683659X-RAY DIFFRACTION100
2.0227-2.04650.32041700.30623692X-RAY DIFFRACTION100
2.0465-2.07150.32911900.2933630X-RAY DIFFRACTION100
2.0715-2.09770.28772100.28353704X-RAY DIFFRACTION100
2.0977-2.12530.29111780.26423648X-RAY DIFFRACTION100
2.1253-2.15440.25442140.25883680X-RAY DIFFRACTION100
2.1544-2.18520.26922180.25123607X-RAY DIFFRACTION100
2.1852-2.21780.27482160.25763661X-RAY DIFFRACTION100
2.2178-2.25250.30772050.25183629X-RAY DIFFRACTION100
2.2525-2.28940.26691950.24273642X-RAY DIFFRACTION99
2.2894-2.32890.29582130.23893661X-RAY DIFFRACTION100
2.3289-2.37120.24881920.22753659X-RAY DIFFRACTION100
2.3712-2.41680.25731950.22213721X-RAY DIFFRACTION100
2.4168-2.46620.26471880.21323661X-RAY DIFFRACTION100
2.4662-2.51980.24831750.21793701X-RAY DIFFRACTION100
2.5198-2.57840.24982000.20863687X-RAY DIFFRACTION100
2.5784-2.64290.25391860.20573670X-RAY DIFFRACTION100
2.6429-2.71430.23581990.20633700X-RAY DIFFRACTION100
2.7143-2.79420.27322040.20763702X-RAY DIFFRACTION100
2.7942-2.88440.24581900.20833669X-RAY DIFFRACTION99
2.8844-2.98740.25531860.23718X-RAY DIFFRACTION99
2.9874-3.1070.23652150.20253663X-RAY DIFFRACTION99
3.107-3.24840.22311840.18993655X-RAY DIFFRACTION98
3.2484-3.41960.21081990.18293677X-RAY DIFFRACTION99
3.4196-3.63380.17441970.17383693X-RAY DIFFRACTION99
3.6338-3.91430.18722010.15943740X-RAY DIFFRACTION99
3.9143-4.3080.17151910.1463730X-RAY DIFFRACTION99
4.308-4.93080.14891690.12633767X-RAY DIFFRACTION99
4.9308-6.21030.16881820.15113762X-RAY DIFFRACTION98
6.2103-48.86510.1691890.17363914X-RAY DIFFRACTION97
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)
11.98850.05911.04810.42440.33912.7465-0.06810.2954-0.0247-0.22860.0682-0.0006-0.16070.14660.06360.3722-0.0153-0.00350.33590.01170.330526.5461226.2283236.1788
22.3919-1.09310.25692.34930.00371.51630.02890.06780.2246-0.0103-0.0151-0.4014-0.17520.20240.00740.2848-0.0649-0.02040.28560.01460.327435.2647238.5641255.1658
31.0669-0.761-0.33332.44480.21751.09490.0203-0.0609-0.03360.0829-0.019-0.01520.0250.1048-0.00230.2176-0.02290.00360.29240.01710.228331.5805229.844258.6508
43.8572-0.15791.79220.6021-0.37672.8093-0.20750.3114-0.15550.07180.22340.20430.0691-0.05680.02650.46240.025-0.09020.4828-0.03360.443515.0282218.5412226.5751
52.00810.24640.32750.48610.02553.3709-0.010.1589-0.1136-0.25690.03410.2257-0.0473-0.3627-0.00360.3420.0169-0.05070.2713-0.02810.3554-5.6892128.1644252.5756
61.04520.06760.03471.20860.48621.08320.0195-0.093-0.1066-0.0314-0.01880.01190.00540.0082-0.00390.2351-0.00290.00380.26260.02460.26848.2024122.4209270.0506
75.77230.17741.95951.3512-1.38323.3580.04140.5525-0.1439-0.20790.1409-0.07920.2917-0.6679-0.07650.43550.0133-0.12850.5136-0.03660.3436-10.8549131.1883242.0049
82.4870.3354-0.18971.77780.57452.7954-0.32350.25180.741-0.00920.5942-0.039-0.71230.493-0.21160.6043-0.0905-0.07840.7066-0.04930.5276-4.1635138.4912233.8964
94.7437-3.8312-1.15715.15721.90383.2010.59230.13880.2061-0.6198-0.2303-0.0628-0.5263-0.0383-0.31180.3108-0.0244-0.05450.31180.02270.282-12.3424160.1656259.7666
102.245-0.7570.65591.2051-0.59110.96920.01780.02510.1496-0.0756-0.05440.00670.13920.01090.04370.25030.012-0.00810.24810.02940.2549-5.7364153.5011264.1088
112.5684-1.664-0.95962.95870.12332.67030.06120.0297-0.1351-0.0732-0.03630.2803-0.08190.0175-0.01170.2414-0.0252-0.01430.2954-0.0030.3363-12.1724148.5356266.5688
122.4633-1.0769-0.49463.30370.24230.07420.01610.11780.33430.06640.0412-0.20450.032-0.1037-0.03480.27010.0048-0.03410.32760.00430.228-3.9906152.537266.028
130.20320.31520.15361.8876-0.43850.3195-0.03740.04650.0382-0.18730.21370.08990.0312-0.0376-0.1450.282-0.02340.00450.3240.04380.2706-7.8439165.1676263.7473
142.7541.249-0.55974.9491-0.62021.4853-0.15050.1389-0.0121-0.03820.2895-0.2148-0.2265-0.0215-0.06610.376-0.0328-0.00980.35090.02720.3273-5.6398190.7538261.2324
152.03640.69690.36583.66960.72920.5462-0.2443-0.0037-0.0401-0.12390.2979-0.05950.03150.0751-0.06370.3435-0.0099-0.00020.31220.01850.3578-3.9909187.7061263.0687
164.08063.1584-0.10586.9996-0.37992.2514-0.67550.28080.4585-1.20.52660.5759-0.4593-0.16990.160.5563-0.0821-0.10660.38510.06560.3954-9.2636191.7833253.645
174.3971-1.3970.33884.69250.5782.9265-0.1660.9501-0.6467-0.5844-0.14480.20060.4231-0.23160.25370.4663-0.04250.08070.36220.01560.282838.2356194.688236.1093
181.6075-0.56720.7463.29350.23641.2610.02490.14050.0022-0.4435-0.0931-0.15470.12760.17930.09130.36990.02370.06940.36110.01330.288737.3507201.5535243.645
194.6912-0.92470.44622.89730.65451.1172-0.08180.28620.0225-0.4942-0.0303-0.397-0.07470.01640.14540.3473-0.02030.09670.36470.03140.361343.2168206.617240.0341
200.7263-0.5651-0.68843.66920.74941.2536-0.05790.1124-0.07320.004-0.0728-0.1790.09180.11170.07140.27520.00390.01930.34110.00470.279636.3257204.1836247.7305
210.63670.33580.19671.10820.17470.0690.10410.67350.121-1.1503-0.0519-0.9239-0.1561-0.064-0.03360.5568-0.02980.21810.4715-0.05430.504643.1126184.0339235.9246
222.98562.5755-0.9975.9301-0.62971.2963-0.16260.37640.0076-0.42440.3533-0.2183-0.0290.0219-0.17610.3675-0.01860.04960.3798-0.01020.349635.7655165.3921243.4991
234.14062.493-0.73828.7907-0.87371.908-0.25140.969-0.0228-1.53730.68640.0610.1709-0.0736-0.34660.6389-0.02780.00210.7309-0.02370.370932.1431162.8871235.2809
243.61072.03090.97055.59460.08731.9318-0.15410.1003-0.2290.05630.0555-0.41970.02390.28220.12190.29350.031-0.00960.32420.02410.324736.111189.6605266.2088
251.63560.2021-0.18492.6219-0.74371.8845-0.0171-0.04860.02330.1207-0.2593-0.4497-0.12870.27330.20730.3202-0.0134-0.03460.31260.03280.340136.2923199.2963263.7684
262.7304-0.1721-1.13733.4009-1.58641.27940.11090.0667-0.0638-0.19720.05420.26640.09150.014-0.15760.32570.0142-0.0280.319-0.00870.29427.8116197.3914261.815
270.8236-0.0894-0.73552.618-1.65071.7893-0.01490.058-0.1627-0.0196-0.0415-0.1819-0.0882-0.04190.05780.30830.0095-0.02680.3026-0.01740.276334.5025195.9948259.0832
280.39780.2790.3165.6814-1.06140.66850.04610.1077-0.13930.342-0.1583-0.2808-0.0447-0.01390.06790.28530.0062-0.03550.3105-0.00170.353631.4445173.9975265.0534
293.7231-0.0063-0.91432.5907-0.0442.9439-0.17250.7735-0.7534-0.52540.1654-0.11790.38420.0640.05380.4005-0.0150.01310.5572-0.14860.596143.8846157.1037243.2839
303.388-1.0258-1.8341.77841.26852.54860.0163-0.0452-0.0432-0.04720.0967-0.3526-0.15130.1448-0.09640.2912-0.0077-0.03520.3265-0.010.430442.6606164.9346256.3888
317.4424-2.067-0.40951.76770.0121.37640.18690.3615-0.16190.0541-0.1352-0.12540.0832-0.1097-0.08260.2795-0.0265-0.00910.2841-0.02860.373740.8255168.5279255.4334
323.6803-0.5647-0.88331.0902-0.09332.2860.02480.4606-0.5977-0.52160.1379-0.74660.3660.401-0.09770.35530.1060.14150.499-0.16880.749251.9766159.5178245.7487
333.7112-0.977-1.61482.97051.27263.4138-0.0194-0.1685-0.4195-0.12450.1708-0.46350.32230.3117-0.1040.33330.0426-0.02090.31330.00990.52145.737156.5176258.6203
345.48433.565-2.13956.7596-2.11914.8123-0.0532-0.52840.21670.2803-0.1928-0.05220.00480.12770.17860.2630.0579-0.03150.2752-0.02030.244912.2411165.7588277.6072
351.91740.23380.10753.6723-0.66182.28390.1716-0.1625-0.00340.2033-0.16270.08370.02310.092-0.04620.2963-0.00750.00990.3079-0.03250.323710.2836156.2783276.1376
362.89720.6371-1.0252.24781.12711.9369-0.04150.0892-0.0981-0.29240.0423-0.048-0.167-0.1080.0260.2690.0098-0.01970.2825-0.00780.295114.247158.1595268.3122
371.97650.43130.44521.79390.04050.19730.0458-0.11040.2582-0.0839-0.11230.05220.11060.07610.01780.28080.01010.00770.3248-0.02470.284212.0932163.9795268.7514
383.40691.43561.03868.22192.15760.7275-0.2274-0.1205-0.11030.55410.38250.4338-0.07530.0067-0.08520.29840.05170.04220.3598-0.00110.25912.0433153.2758275.8907
390.0722-0.1511-0.02987.09130.66480.06950.0457-0.17040.33840.31070.02470.0833-0.1363-0.0621-0.08140.2921-0.0254-0.00470.341-0.01430.355613.9644181.7199272.8692
406.60180.6150.68143.62810.76033.50.29330.36780.4191-0.1456-0.12550.5128-0.3594-0.5175-0.11590.51630.09110.01530.36560.03670.4354-11.0714197.7359267.5128
416.0983-2.8784-1.912.33671.06230.6669-0.1187-0.2952-0.06240.35740.20670.1296-0.05730.1869-0.06630.35690.01810.06060.35420.06080.3747-0.1796190.7538275.671
422.9458-1.8199-1.78372.49112.47313.943-0.07250.1781-0.15490.25860.00230.2085-0.0584-0.26840.01590.30290.03010.03430.34710.10710.3860.4588187.1741273.8461
434.3159-1.58440.37032.85620.38282.2318-0.3335-0.55260.23970.30280.3540.3375-0.1004-0.31890.00960.43740.09240.10830.41540.05440.4009-5.9077197.8162277.533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 40 through 115 )
2X-RAY DIFFRACTION2chain 'D' and (resid 116 through 175 )
3X-RAY DIFFRACTION3chain 'D' and (resid 176 through 265 )
4X-RAY DIFFRACTION4chain 'D' and (resid 266 through 312 )
5X-RAY DIFFRACTION5chain 'A' and (resid 40 through 115 )
6X-RAY DIFFRACTION6chain 'A' and (resid 116 through 265 )
7X-RAY DIFFRACTION7chain 'A' and (resid 266 through 288 )
8X-RAY DIFFRACTION8chain 'A' and (resid 289 through 311 )
9X-RAY DIFFRACTION9chain 'H' and (resid 1 through 17 )
10X-RAY DIFFRACTION10chain 'H' and (resid 18 through 51 )
11X-RAY DIFFRACTION11chain 'H' and (resid 52 through 83 )
12X-RAY DIFFRACTION12chain 'H' and (resid 84 through 109 )
13X-RAY DIFFRACTION13chain 'H' and (resid 110 through 140 )
14X-RAY DIFFRACTION14chain 'H' and (resid 141 through 173 )
15X-RAY DIFFRACTION15chain 'H' and (resid 174 through 204 )
16X-RAY DIFFRACTION16chain 'H' and (resid 205 through 229 )
17X-RAY DIFFRACTION17chain 'G' and (resid 1 through 17 )
18X-RAY DIFFRACTION18chain 'G' and (resid 18 through 51 )
19X-RAY DIFFRACTION19chain 'G' and (resid 52 through 83 )
20X-RAY DIFFRACTION20chain 'G' and (resid 84 through 119 )
21X-RAY DIFFRACTION21chain 'G' and (resid 120 through 135 )
22X-RAY DIFFRACTION22chain 'G' and (resid 136 through 204 )
23X-RAY DIFFRACTION23chain 'G' and (resid 205 through 230 )
24X-RAY DIFFRACTION24chain 'I' and (resid 1 through 18 )
25X-RAY DIFFRACTION25chain 'I' and (resid 19 through 38 )
26X-RAY DIFFRACTION26chain 'I' and (resid 39 through 75 )
27X-RAY DIFFRACTION27chain 'I' and (resid 76 through 103 )
28X-RAY DIFFRACTION28chain 'I' and (resid 104 through 114 )
29X-RAY DIFFRACTION29chain 'I' and (resid 115 through 129 )
30X-RAY DIFFRACTION30chain 'I' and (resid 130 through 151 )
31X-RAY DIFFRACTION31chain 'I' and (resid 152 through 175 )
32X-RAY DIFFRACTION32chain 'I' and (resid 176 through 189 )
33X-RAY DIFFRACTION33chain 'I' and (resid 190 through 212 )
34X-RAY DIFFRACTION34chain 'J' and (resid 1 through 18 )
35X-RAY DIFFRACTION35chain 'J' and (resid 19 through 38 )
36X-RAY DIFFRACTION36chain 'J' and (resid 39 through 75 )
37X-RAY DIFFRACTION37chain 'J' and (resid 76 through 91 )
38X-RAY DIFFRACTION38chain 'J' and (resid 92 through 103 )
39X-RAY DIFFRACTION39chain 'J' and (resid 104 through 114 )
40X-RAY DIFFRACTION40chain 'J' and (resid 115 through 129 )
41X-RAY DIFFRACTION41chain 'J' and (resid 130 through 151 )
42X-RAY DIFFRACTION42chain 'J' and (resid 152 through 175 )
43X-RAY DIFFRACTION43chain 'J' and (resid 176 through 212 )

+
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