[English] 日本語
Yorodumi
- PDB-4n5k: Crystal structure of hemagglutinin from an H7N9 influenza virus i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n5k
TitleCrystal structure of hemagglutinin from an H7N9 influenza virus in complex with LSTa
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / viral envelope protein / hemagglutinin / viral fusion protein
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / metal ion binding
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
N-acetyl-alpha-neuraminic acid / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7053 Å
AuthorsXu, R. / Wilson, I.A.
CitationJournal: Science / Year: 2013
Title: Preferential recognition of avian-like receptors in human influenza A H7N9 viruses.
Authors: Xu, R. / de Vries, R.P. / Zhu, X. / Nycholat, C.M. / McBride, R. / Yu, W. / Paulson, J.C. / Wilson, I.A.
History
DepositionOct 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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 / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin HA1
B: Hemagglutinin HA2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,54610
Polymers111,5154
Non-polymers2,0316
Water50428
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules

A: Hemagglutinin HA1
B: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,77318
Polymers167,2726
Non-polymers4,50112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area36460 Å2
ΔGint-102 kcal/mol
Surface area59450 Å2
MethodPISA
2
C: Hemagglutinin HA1
D: Hemagglutinin HA2
hetero molecules

C: Hemagglutinin HA1
D: Hemagglutinin HA2
hetero molecules

C: Hemagglutinin HA1
D: Hemagglutinin HA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,86412
Polymers167,2726
Non-polymers1,5916
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area33090 Å2
ΔGint-149 kcal/mol
Surface area58150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.698, 154.698, 154.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-311-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA - B11 - 541
211chain CC - D11 - 541
112chain BB4 - 172
212chain DD4 - 172

NCS ensembles :
ID
1
2

-
Components

-
Hemagglutinin ... , 2 types, 4 molecules ACBD

#1: Protein Hemagglutinin HA1


Mass: 34993.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/2/2013 / Gene: HA, hemagglutinin / Plasmid: pFastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: R4NN21
#2: Protein Hemagglutinin HA2


Mass: 20763.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/2/2013 / Gene: HA, hemagglutinin / Plasmid: pFastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: R4NN21

-
Sugars , 4 types, 6 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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
#6: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 1 types, 28 molecules

#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 17-20% PEG3350, 0.2 M ammonium acetate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295.5K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2013 / Details: K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 5.5 % / Number: 187164 / Rmerge(I) obs: 0.076 / Χ2: 1.05 / D res high: 2.7 Å / D res low: 50 Å / Num. obs: 33887 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.815099.110.0371.0815.3
4.625.8199.910.051.0595.7
4.034.6299.710.060.9815.4
3.664.0310010.0911.0685.7
3.43.6699.910.131.0645.3
3.23.499.910.161.0995.5
3.043.299.910.2551.0845.7
2.913.0410010.3851.0335.8
2.82.9199.910.5821.0675.2
2.72.899.910.8630.975.5
ReflectionResolution: 2.7→50 Å / Num. obs: 33887 / % possible obs: 99.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.076

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.31 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.75 Å48.92 Å
Translation2.75 Å48.92 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7053→48.92 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.41 / σ(F): 0 / Phase error: 30.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2761 1718 5.07 %
Rwork0.227 --
obs0.2296 33861 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.5868 Å2
Refinement stepCycle: LAST / Resolution: 2.7053→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7600 0 132 28 7760
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037891
X-RAY DIFFRACTIONf_angle_d0.72210651
X-RAY DIFFRACTIONf_dihedral_angle_d16.0992934
X-RAY DIFFRACTIONf_chiral_restr0.0481168
X-RAY DIFFRACTIONf_plane_restr0.0031399
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A2994X-RAY DIFFRACTIONTORSIONAL
12C2994X-RAY DIFFRACTIONTORSIONAL
21B1640X-RAY DIFFRACTIONTORSIONAL
22D1640X-RAY DIFFRACTIONTORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7053-2.78490.43021190.36152683X-RAY DIFFRACTION100
2.7849-2.87470.38021460.33152641X-RAY DIFFRACTION100
2.8747-2.97750.3631310.30092668X-RAY DIFFRACTION100
2.9775-3.09670.34261360.28692673X-RAY DIFFRACTION100
3.0967-3.23760.33191370.28942648X-RAY DIFFRACTION100
3.2376-3.40820.29591360.25972657X-RAY DIFFRACTION100
3.4082-3.62170.28251710.24792660X-RAY DIFFRACTION100
3.6217-3.90120.28751390.22972666X-RAY DIFFRACTION100
3.9012-4.29360.26441530.19982675X-RAY DIFFRACTION100
4.2936-4.91440.23491500.18122658X-RAY DIFFRACTION100
4.9144-6.18970.24111510.20272742X-RAY DIFFRACTION100
6.1897-48.92780.25741490.20432772X-RAY DIFFRACTION99
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)
13.79332.9399-3.90186.3442-5.27068.04560.23730.10210.74080.33720.49881.0559-0.4125-0.5675-0.70940.36580.00970.06320.4056-0.02510.6095-2.2002-57.34630.8425
24.26182.8826-2.23772.0179-1.51830.9580.6507-0.48610.56860.326-0.20790.6502-0.25080.2859-0.47210.6948-0.12590.0770.6022-0.11160.757835.8788-28.2678-15.8016
36.47041.1492-0.15551.9633-1.34031.17040.34950.1521-0.40580.4481-0.7664-0.2769-0.70321.46230.46820.6336-0.1963-0.02831.03770.00030.541557.6748-23.3581-23.3059
45.6031.12991.17956.4018-3.30635.81770.45530.4730.24550.4844-0.37840.5813-0.69311.6443-0.04570.6028-0.20950.03081.0404-0.18070.574554.0153-20.1223-28.6983
53.2594-1.06230.28096.5768-3.10943.49960.08471.1688-0.1499-1.11130.3501-0.12560.52171.3182-0.40650.8174-0.0447-0.21861.5021-0.21880.716552.5995-23.3114-40.3855
60.8548-0.63611.55526.6984-5.03516.5504-0.00640.5062-0.040.37390.55010.9544-0.25490.8983-0.4690.548-0.0832-0.14490.9107-0.02780.71543.0803-21.5064-34.8924
72.3409-0.00790.11293.2056-0.65663.76290.50030.3215-0.63770.3596-0.4019-0.07390.38451.0396-0.10580.5254-0.0004-0.16560.9024-0.17330.627351.8276-31.0577-23.882
84.14071.56910.67674.39452.58052.61610.7135-0.57660.0991.4293-0.49320.082-0.67670.1716-0.11450.9641-0.2460.28920.7662-0.14240.865526.1811-32.7121-5.9184
96.32712.0283-1.35354.5537-0.23862.70810.5259-0.11390.6312-0.0746-0.42850.0826-0.31760.5919-0.02590.6335-0.07590.10510.4903-0.06590.708620.9337-43.3842-11.0948
105.64093.1251-3.52595.3857-1.90052.8328-0.15950.61850.86470.02680.69180.5199-0.1335-1.464-0.63050.41290.01880.04660.5812-0.00950.73491.055-53.0535-3.4118
112.754-2.4945-3.32143.43691.97134.96790.05060.19860.02830.7858-0.33650.4270.1671-2.21310.46560.45080.02160.25410.8769-0.10570.8701-12.2734-65.51798.1912
125.16681.373-4.31222.4879-2.17354.90020.1886-0.80550.34690.50230.09850.1281-0.821-0.3027-0.3230.6134-0.02590.19310.8448-0.12130.5185-6.1393-62.721717.1069
139.60223.5429-3.21488.4085-2.97828.01110.0264-1.955-1.04980.4959-1.152-0.9447-0.15590.92940.84470.6538-0.0580.01481.07350.02920.642911.8473-61.51796.7903
144.95524.233-5.05523.9666-4.07565.22520.1626-2.6707-1.26491.0325-1.1476-1.0378-0.37911.01650.59591.0546-0.02890.04361.32490.14491.043727.7732-49.4791-8.6915
154.92250.12310.22664.71252.36589.64540.2030.64670.2747-0.2328-0.34240.1895-0.96010.528-0.07580.8803-0.09120.14040.6501-0.00860.795828.9168-33.4718-25.5189
164.7953.2397-5.4691.6404-3.76016.5443-0.1423-0.0457-0.0105-0.01160.05390.0170.1805-0.02170.16220.6083-0.04020.11230.4968-0.04120.590710.7115-59.2603-9.4502
172.7895-0.32881.62115.4175-0.12824.983-0.1051-0.5176-0.06030.20110.0680.11830.7911-0.64180.08530.6765-0.08490.16910.84330.06710.5529-9.3545-79.64120.881
181.8437-0.0746-0.40582.0150.63251.95570.22230.0872-0.6084-0.18570.48680.67081.2762-0.4441-0.01982.163-1.9835-0.2432.0492-1.3212.2818-34.3474-40.8189-16.5784
190.7665-0.33790.9590.2469-0.43451.2381-0.74480.3492-0.87790.06260.43860.34130.9065-0.98380.02281.5987-0.5413-0.43931.1611-0.5621.9453-1.8401-31.54414.3247
205.4631-0.83420.25823.02451.99035.0270.6768-0.03-0.7157-0.5947-0.3661-0.04221.0648-0.2769-0.28051.3936-0.0359-0.23950.7915-0.20321.252313.7832-15.92099.8706
216.1728-2.0786-0.08314.6273.17845.95020.8981-0.74420.6387-0.5072-0.3342-1.149-0.385-0.2639-0.57870.8841-0.12210.16040.8365-0.29891.060821.6157-3.20714.8673
226.654-2.7875-0.45537.03764.94263.76210.7606-1.07010.2425-0.6562-0.57350.12070.2893-1.2301-0.30480.9063-0.16490.0481.0926-0.35330.982411.1578-3.31217.2108
236.4269-0.3287-0.46653.21610.84955.16570.81190.8130.1512-0.8032-0.2486-0.35490.58770.0748-0.43711.14810.19950.06610.6691-0.14350.895719.1607-10.24643.9681
240.4796-0.0070.06070.0244-0.01070.23240.29010.3858-1.69810.0260.1011.06591.5691.13450.06741.6586-0.3574-0.4111.5152-0.60631.8468-2.8163-32.66523.5137
251.20650.98420.00441.5221-0.59670.5232-0.26820.1008-0.70480.8307-0.64340.22420.3706-0.09290.27541.946-1.3101-0.97751.1175-0.76921.6461-11.1704-27.0046-4.7147
261.36151.7494-0.08862.6411-0.1181.1404-0.33340.7904-0.40730.05680.30070.7241-0.1565-0.58370.45451.4157-1.4628-0.22192.3465-0.99361.9909-30.9949-36.8943-12.0243
270.28920.2760.10330.36940.09850.0487-0.40870.4810.7057-0.94110.61411.4489-0.12970.1165-0.36971.7393-0.3012-0.43251.3843-0.63923.756-44.5386-48.6435-24.0917
280.5227-0.1715-0.53871.22070.22830.6466-0.3494-1.31891.1874-0.31810.32050.3798-0.14841.73130.01712.2572-0.6092-0.31882.4772-0.88382.755-36.9039-56.4915-24.2126
292.5063-0.40050.14711.7389-1.72597.4461-1.1017-0.25220.70380.31280.2526-1.43590.0820.49870.02061.8103-0.4447-0.48071.8944-1.4233.265-20.6721-43.3281-24.0122
304.40012.41252.27843.16871.26595.08490.6869-0.2874-1.81240.3994-0.5114-0.83470.0732-0.71450.09511.4266-0.1486-0.34481.1262-0.50611.6114-4.457-20.2554-2.9599
311.5810.3524-0.03241.2691.38221.2211-0.91630.5584-0.5567-0.43480.07790.69660.804-1.31850.29662.3502-1.7197-0.46482.0375-0.76811.8611-23.9772-28.042-18.5692
323.6443-2.2065-3.93912.8043.074.5741-0.18541.3678-0.2345-0.65580.31610.87850.87-0.18290.47122.8726-0.5358-0.57262.6161-1.50533.2392-44.9129-50.7422-38.2951
330.2387-0.1025-0.12080.7648-0.03860.1144-0.0057-0.14410.38210.09570.0388-0.1244-0.2125-0.0780.00882.7247-1.2481-1.5932.6042-1.36693.6712-45.0609-59.8022-37.6175
340.4775-0.5745-0.65010.75260.65321.2305-0.2283-0.5571-0.5153-0.1812-0.48550.03170.1453-0.20790.37721.8363-0.312-0.52012.3826-1.10053.4441-35.6607-62.7326-34.4509
350.6411-0.76070.39721.20620.05771.1378-1.29930.18850.3158-0.51310.3790.0382-1.32710.27320.23841.9923-0.4982-0.01022.0632-1.69523.8647-35.3867-60.3155-43.3239
363.2807-0.7606-1.11271.44241.50531.6009-0.26960.66410.8691-0.5442-0.27990.9097-0.5520.04390.2512.3297-0.9330.05921.7659-0.64862.4843-49.8194-58.7736-47.4186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 114 )
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 132 )
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 184 )
5X-RAY DIFFRACTION5chain 'A' and (resid 185 through 213 )
6X-RAY DIFFRACTION6chain 'A' and (resid 214 through 237 )
7X-RAY DIFFRACTION7chain 'A' and (resid 238 through 269 )
8X-RAY DIFFRACTION8chain 'A' and (resid 270 through 288 )
9X-RAY DIFFRACTION9chain 'A' and (resid 289 through 308 )
10X-RAY DIFFRACTION10chain 'A' and (resid 309 through 327 )
11X-RAY DIFFRACTION11chain 'B' and (resid 4 through 13 )
12X-RAY DIFFRACTION12chain 'B' and (resid 14 through 37 )
13X-RAY DIFFRACTION13chain 'B' and (resid 38 through 54 )
14X-RAY DIFFRACTION14chain 'B' and (resid 55 through 64 )
15X-RAY DIFFRACTION15chain 'B' and (resid 65 through 74 )
16X-RAY DIFFRACTION16chain 'B' and (resid 75 through 126 )
17X-RAY DIFFRACTION17chain 'B' and (resid 127 through 172 )
18X-RAY DIFFRACTION18chain 'C' and (resid 11 through 41 )
19X-RAY DIFFRACTION19chain 'C' and (resid 42 through 65 )
20X-RAY DIFFRACTION20chain 'C' and (resid 66 through 132 )
21X-RAY DIFFRACTION21chain 'C' and (resid 133 through 213 )
22X-RAY DIFFRACTION22chain 'C' and (resid 214 through 237 )
23X-RAY DIFFRACTION23chain 'C' and (resid 238 through 269 )
24X-RAY DIFFRACTION24chain 'C' and (resid 270 through 288 )
25X-RAY DIFFRACTION25chain 'C' and (resid 289 through 308 )
26X-RAY DIFFRACTION26chain 'C' and (resid 309 through 327 )
27X-RAY DIFFRACTION27chain 'D' and (resid 4 through 13 )
28X-RAY DIFFRACTION28chain 'D' and (resid 14 through 37 )
29X-RAY DIFFRACTION29chain 'D' and (resid 38 through 54 )
30X-RAY DIFFRACTION30chain 'D' and (resid 55 through 74 )
31X-RAY DIFFRACTION31chain 'D' and (resid 75 through 126 )
32X-RAY DIFFRACTION32chain 'D' and (resid 127 through 137 )
33X-RAY DIFFRACTION33chain 'D' and (resid 138 through 145 )
34X-RAY DIFFRACTION34chain 'D' and (resid 146 through 153 )
35X-RAY DIFFRACTION35chain 'D' and (resid 154 through 162 )
36X-RAY DIFFRACTION36chain 'D' and (resid 163 through 172 )

+
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