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- PDB-4cqy: H5 (tyTy) Del133/Ile155Thr Mutant Haemagglutinin in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 4cqy
TitleH5 (tyTy) Del133/Ile155Thr Mutant Haemagglutinin in Complex with Avian Receptor Analogue LSTa
Components(HAEMAGGLUTININ ...) x 2
KeywordsVIRAL PROTEIN / SIALIC ACID / GLYCOPROTEIN / VIRUS RECEPTOR / AVIAN FLU / SIALYLLACTOSAMINE / 3SLN / 3'SLN / 6SLN / 6'SLN / LSTA
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 / 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 / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Hemagglutinin
Similarity search - Component
Biological speciesINFLUENZA A VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsXiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / McCauley, J.W. ...Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / McCauley, J.W. / Gamblin, S.J. / Skehel, J.J.
CitationJournal: Virology / Year: 2014
Title: Enhanced Human Receptor Binding by H5 Haemagglutinins.
Authors: Xiong, X. / Xiao, H. / Martin, S.R. / Coombs, P.J. / Liu, J. / Collins, P.J. / Vachieri, S.G. / Walker, P.A. / Lin, Y.P. / Mccauley, J.W. / Gamblin, S.J. / Skehel, J.J.
History
DepositionFeb 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HAEMAGGLUTININ HA1
B: HAEMAGGLUTININ HA2
C: HAEMAGGLUTININ HA1
D: HAEMAGGLUTININ HA2
E: HAEMAGGLUTININ HA1
F: HAEMAGGLUTININ HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,61520
Polymers168,4106
Non-polymers4,20514
Water23,6721314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32680 Å2
ΔGint-122.6 kcal/mol
Surface area60750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.000, 116.350, 101.840
Angle α, β, γ (deg.)90.00, 91.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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HAEMAGGLUTININ ... , 2 types, 6 molecules ACEBDF

#1: Protein HAEMAGGLUTININ HA1


Mass: 37010.672 Da / Num. of mol.: 3
Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-342
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS (A/TURKEY/TURKEY/1/2005(H5N1))
Variant: DEL133/ILE155THR MUTANT / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q207Z6
#2: Protein HAEMAGGLUTININ HA2


Mass: 19126.004 Da / Num. of mol.: 3
Fragment: HA2 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) INFLUENZA A VIRUS (A/TURKEY/TURKEY/1/2005(H5N1))
Variant: DEL133/ILE155THR MUTANT / Plasmid: PACGP67A / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q207Z6

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Sugars , 2 types, 12 molecules

#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: 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.: 9
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

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Non-polymers , 2 types, 1316 molecules

#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1314 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsMULTIBASIC SITE REMOVED

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: BIS-TRIS PROPANE PH 7.5, 0.05 - 0.15 M K/NAPO4 (PH 7.0), 15-18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.05→48.69 Å / Num. obs: 125504 / % possible obs: 96.6 % / Observed criterion σ(I): 1.94 / Redundancy: 3.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.07
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.94 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BGZ

4bgz


Resolution: 2.05→48.74 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.581 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22671 6342 5.1 %RANDOM
Rwork0.19269 ---
obs0.19442 119124 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.036 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å2-0 Å2-1.21 Å2
2---1.53 Å2-0 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.05→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11638 0 274 1314 13226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01912210
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0951.96316580
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56651452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30325.097616
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.083152023
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4461558
X-RAY DIFFRACTIONr_chiral_restr0.0680.21797
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219362
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3811.3575826
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.672.0337272
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8731.5486384
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 442 -
Rwork0.28 8672 -
obs--95.38 %
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)
13.5151-0.82532.80971.35270.11444.51080.12490.1756-0.1622-0.04210.04050.10220.26190.2353-0.16540.2153-0.00880.01980.1343-0.04110.1176-18.2303-26.7357-18.704
21.71670.61891.18992.4111.38983.53060.13990.391-0.23450.23520.1466-0.43310.34240.4544-0.28650.07570.06310.0230.264-0.11880.284726.1704-20.021326.1005
37.03082.55013.38790.93761.24032.5846-0.18490.62440.0762-0.11250.17520.008-0.18090.77670.00970.2350.09880.05660.5051-0.06530.22227.7553-22.68951.5646
45.9245-1.65236.58062.1693-0.283914.68830.3788-0.0942-0.6339-0.20010.07660.11950.5609-0.7703-0.45550.19830.00150.02840.2025-0.04390.1966-18.0115-27.1328-14.2817
53.4189-0.4462-1.47593.30153.19627.36880.13250.4472-0.068-0.3258-0.04790.0698-0.0617-0.3581-0.08460.23910.0361-0.0210.19980.01120.1251-26.1378-22.2496-33.0123
66.11031.38745.27376.04093.779421.5524-0.1690.18730.12980.11610.0556-0.462-0.50240.96680.11340.1889-0.02720.05560.20240.01370.3175-13.7464-12.0124-18.3212
75.4751-0.65474.12542.30960.764111.31630.16280.7122-0.2965-0.3843-0.0106-0.09460.16590.95-0.15220.16090.0060.05550.1231-0.02270.14720.0586-18.493317.9253
83.2682-0.15624.9130.9751-0.196110.6688-0.08620.2060.177-0.2714-0.09930.215-0.2385-0.27790.18540.2150.06460.01520.2026-0.01630.2093-27.1872-14.9503-25.6187
91.1477-0.35091.44160.381-0.68482.6877-0.0095-0.107-0.04710.06220.08490.1384-0.001-0.5169-0.07540.148-0.00910.0740.22350.03690.1742-25.1698-21.473626.4461
101.63920.52720.80952.9530.92171.58590.1682-0.0738-0.12590.18290.0194-0.41170.12850.0233-0.18760.2128-0.0243-0.00320.04490.05310.15622.9882-26.232951.2733
113.1069-2.05142.57862.5842-2.64973.05580.0344-0.0202-0.22980.04740.11110.06310.1621-0.2495-0.14550.2401-0.07240.03660.25920.08180.1594-24.2956-24.676827.4624
127.21271.16417.46220.61160.596410.8368-0.2894-0.07530.3167-0.05120.04420.2171-0.2759-0.28780.24520.1271-0.04810.06940.30880.04960.1905-33.7788-16.67598.5225
138.62960.48650.51434.1697-1.18734.14130.1892-0.1438-0.4537-0.29690.13680.9370.5829-1.6606-0.3260.2591-0.1743-0.03530.7590.05120.4556-51.1605-19.4654-12.6017
1421.3750.25219.37844.14-0.0128.50670.8827-0.2788-1.0280.1265-0.03690.00341.1585-0.2539-0.84580.3552-0.04380.06960.26080.08430.2863-35.8125-26.3616-4.0654
1510.47671.993110.32610.67391.944210.21820.1635-0.0106-0.26130.06790.09890.0630.1665-0.1046-0.26240.1269-0.01890.06720.22940.03340.1346-22.9221-14.24827.3651
163.6021.82673.94567.48960.284211.01980.84190.3479-0.8598-1.18860.06780.97082.0229-0.9311-0.90970.745-0.1254-0.44360.9644-0.04750.8131-53.645-24.5386-27.6511
171.77570.87663.21510.81851.34966.3025-0.31480.1380.2276-0.20940.04860.1367-0.4640.090.26620.2679-0.0349-0.0270.10880.05840.1644-10.988311.18537.6538
180.8572-0.2164-0.02190.95810.24031.1664-0.07110.10090.0786-0.1022-0.0507-0.0618-0.05510.03280.12180.2376-0.0049-0.01250.0259-0.01240.10613.54417.738237.0846
191.8762-0.0810.13181.2653-0.2251.77-0.0829-0.0481-0.00220.161-0.0029-0.0862-0.07030.11310.08580.20090.0024-0.01690.0104-0.00530.092610.83385.665844.8014
203.31221.25534.48961.39832.68667.655-0.0878-0.03580.1682-0.2138-0.03240.0517-0.3048-0.1820.12020.2804-0.0577-0.02940.11030.04990.1641-12.43548.98135.8697
213.07210.46211.81623.16490.48838.3312-0.42420.08650.5686-0.4128-0.05490.6277-1.3041-0.59220.4790.46990.0272-0.15480.22320.04240.4404-36.10885.0412-16.6513
2210.5832-2.56227.26664.196-1.64187.7959-0.248-0.01290.6152-0.18820.05330.1701-0.2488-0.26360.19470.2472-0.02190.06780.08420.00920.1284-2.7647-5.701217.7321
239.8809-1.53699.18961.0707-1.3710.09650.16240.1622-0.217-0.23160.0380.31170.1394-0.1212-0.20040.2926-0.0255-0.04040.09830.03370.2303-29.4371-4.7255-12.4057
2414.8709-2.6096-18.60022.91630.040227.6725-0.44171.0773-0.3919-0.0920.1290.40010.0806-2.23570.31271.25890.1696-0.7551.1993-0.28371.5882-53.18163.9613-28.3303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 39
2X-RAY DIFFRACTION2A40 - 254
3X-RAY DIFFRACTION3A255 - 304
4X-RAY DIFFRACTION4A305 - 323
5X-RAY DIFFRACTION5B1 - 37
6X-RAY DIFFRACTION6B38 - 59
7X-RAY DIFFRACTION7B60 - 82
8X-RAY DIFFRACTION8B83 - 166
9X-RAY DIFFRACTION9C-1 - 103
10X-RAY DIFFRACTION10C104 - 256
11X-RAY DIFFRACTION11C257 - 299
12X-RAY DIFFRACTION12C300 - 323
13X-RAY DIFFRACTION13D1 - 31
14X-RAY DIFFRACTION14D32 - 61
15X-RAY DIFFRACTION15D62 - 124
16X-RAY DIFFRACTION16D125 - 166
17X-RAY DIFFRACTION17E-1 - 84
18X-RAY DIFFRACTION18E85 - 122
19X-RAY DIFFRACTION19E123 - 266
20X-RAY DIFFRACTION20E267 - 323
21X-RAY DIFFRACTION21F1 - 57
22X-RAY DIFFRACTION22F58 - 83
23X-RAY DIFFRACTION23F84 - 136
24X-RAY DIFFRACTION24F137 - 166

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  • 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

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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

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