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- PDB-4kdm: Crystal structure of the hemagglutinin of ferret-transmissible H5... -

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Basic information

Entry
Database: PDB / ID: 4kdm
TitleCrystal structure of the hemagglutinin of ferret-transmissible H5N1 virus
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / homotrimer / virus attachment and membrane fusion
Function / homology
Function and homology information


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 / identical protein binding / 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
Biological speciesInfluenza A virus
influenza virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.496 Å
AuthorsLu, X. / Shi, Y. / Zhang, W. / Zhang, Y. / Qi, J. / Gao, G.F.
CitationJournal: Protein Cell / Year: 2013
Title: Structure and receptor-binding properties of an airborne transmissible avian influenza A virus hemagglutinin H5 (VN1203mut).
Authors: Lu, X. / Shi, Y. / Zhang, W. / Zhang, Y. / Qi, J. / Gao, G.F.
History
DepositionApr 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Oct 29, 2014Group: Structure summary
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_src_gen / 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_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_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,79012
Polymers169,8536
Non-polymers1,9376
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33770 Å2
ΔGint-139 kcal/mol
Surface area61030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.758, 243.848, 71.614
Angle α, β, γ (deg.)90.00, 110.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hemagglutinin


Mass: 36447.383 Da / Num. of mol.: 3 / Fragment: Residues 17-337 / Mutation: N170D, N236K, Q238L, T331I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: (A/Viet Nam/1203/2004(H5N1)) / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6DQ33
#2: Protein Hemagglutinin


Mass: 20170.232 Da / Num. of mol.: 3 / Fragment: Residues 347-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: (A/Viet Nam/1203/2004(H5N1)) / Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6DQ33
#3: 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.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) influenza virus / Production host: Spodoptera frugiperda (fall armyworm)
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
#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.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Source: (gene. exp.) influenza virus / Production host: Spodoptera frugiperda (fall armyworm)
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.22 Å3/Da / Density % sol: 61.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M sodium cacodylate pH6.0 15% w/v PEG 4,000, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.496→50 Å / Num. all: 73995 / Num. obs: 73995 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.5→2.59 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.496→35.066 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 29.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 3722 5.03 %RANDOM
Rwork0.2151 ---
all0.217 73934 --
obs0.217 73934 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.496→35.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11925 0 126 170 12221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512345
X-RAY DIFFRACTIONf_angle_d1.08316683
X-RAY DIFFRACTIONf_dihedral_angle_d19.0754608
X-RAY DIFFRACTIONf_chiral_restr0.0811791
X-RAY DIFFRACTIONf_plane_restr0.0042169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4957-2.52730.39111240.31882523X-RAY DIFFRACTION96
2.5273-2.56060.381470.30972678X-RAY DIFFRACTION100
2.5606-2.59560.33121510.3022508X-RAY DIFFRACTION100
2.5956-2.63270.30431320.28932620X-RAY DIFFRACTION100
2.6327-2.6720.34061290.2912657X-RAY DIFFRACTION100
2.672-2.71370.36291020.29162586X-RAY DIFFRACTION100
2.7137-2.75820.36531380.28142651X-RAY DIFFRACTION100
2.7582-2.80570.2931250.27652611X-RAY DIFFRACTION100
2.8057-2.85670.31681360.27172620X-RAY DIFFRACTION100
2.8567-2.91160.29711400.26032611X-RAY DIFFRACTION100
2.9116-2.9710.33811450.26352604X-RAY DIFFRACTION100
2.971-3.03560.2931380.27252602X-RAY DIFFRACTION100
3.0356-3.10620.3031550.26332576X-RAY DIFFRACTION100
3.1062-3.18380.30691640.25542613X-RAY DIFFRACTION100
3.1838-3.26980.29611380.25142586X-RAY DIFFRACTION100
3.2698-3.3660.2951250.24372630X-RAY DIFFRACTION100
3.366-3.47450.28641480.23232621X-RAY DIFFRACTION100
3.4745-3.59860.27521460.22512578X-RAY DIFFRACTION100
3.5986-3.74250.21191290.20352637X-RAY DIFFRACTION100
3.7425-3.91260.20991360.20032611X-RAY DIFFRACTION100
3.9126-4.11860.17051230.18842620X-RAY DIFFRACTION100
4.1186-4.37620.24531360.182599X-RAY DIFFRACTION99
4.3762-4.71340.18431310.17162567X-RAY DIFFRACTION97
4.7134-5.18630.23521540.17922557X-RAY DIFFRACTION98
5.1863-5.93370.24271530.18482572X-RAY DIFFRACTION99
5.9337-7.46390.21781310.20592638X-RAY DIFFRACTION100
7.4639-35.06930.20451460.17672536X-RAY DIFFRACTION96
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)
10.13710.08530.00130.05720.00560.01670.0279-0.0143-0.07720.296-0.11080.26690.08880.1006-0.01150.42360.0350.060.2020.01070.269418.844428.63496.8499
20.38450.05210.1160.23260.15610.35610.11270.02020.07310.1948-0.08840.0673-0.0210.007300.2697-0.02480.06580.23180.01280.203420.546865.23015.0239
30.0051-0.00390.00490.0172-0.0104-0.00210.02280.0127-0.12120.15660.01940.02980.14730.091200.3360.02380.02810.2063-0.030.390918.671120.12120.264
40.1285-0.0076-0.1330.0096-0.0060.1089-0.06530.08-0.04980.22140.08930.05270.15590.02290.00380.54870.0789-0.04570.2367-0.03540.366525.75532.9216-1.7995
50.17310.1259-0.01830.0894-0.0098-0.07720.03180.091-0.13720.1775-0.09380.1130.00540.0415-0.00010.41260.0938-0.05020.2518-0.06180.388326.529-8.0375-8.3485
60.1894-0.0079-0.00130.0911-0.11760.2303-0.04680.2372-0.05610.00410.0104-0.190.04420.2241-0.00010.20760.10090.03580.4062-0.00950.169737.091638.5459-26.9025
70.4313-0.1461-0.0020.10640.02830.43110.050.15050.3485-0.14870.0861-0.0066-0.20310.03930.06580.2649-0.01740.01640.44150.11250.252626.600172.9203-27.8707
80.0473-0.0336-0.04730.02420.00990.037-0.01350.1363-0.1084-0.2039-0.0092-0.25450.15370.25080.00030.38130.10130.0020.4209-0.03890.324837.798628.7856-24.7137
90.0025-0.00110.00350.00840.00410.00620.11470.0109-0.0306-0.00310.0536-0.11550.01420.0201-00.88620.24450.03270.665-0.16910.749641.0774-6.3436-22.4252
100.1970.0148-0.09820.1229-0.17250.2469-0.08920.119-0.0380.0083-0.05350.05650.2510.1435-0.25620.4130.15710.01690.2552-0.09570.156831.450610.6138-23.287
11-0.0004-0.00070.00030.01110.00880.005-0.01190.0253-0.0226-0.0257-0.0448-0.03340.0709-0.001301.28110.30470.28940.7137-0.070.883540.3934-22.0255-32.7056
120.00190.00450.00230.00860.00360.0010.0055-0.0452-0.0798-0.01940.05730.00470.01370.005301.48290.09510.1130.7843-0.28881.162736.7721-34.9382-30.0822
130.22060.2228-0.07650.2216-0.11220.30150.17460.3216-0.085-0.20580.04920.27990.1591-0.13880.41110.38620.022-0.21770.4435-0.1690.44690.952727.8697-28.2683
140.35160.00770.13670.16720.02690.25110.09370.17460.23880.0542-0.05320.20550.0453-0.090.02560.02260.0670.00950.33440.12110.4406-4.616165.2013-17.3903
150.12860.034-0.10090.01840.00470.17070.07190.0968-0.0961-0.18690.05370.10090.10710.01090.05880.36310.0086-0.14280.4024-0.10540.45954.413723.8563-27.0441
160.00160.00850.0005-0.00060.00120.0064-0.06230.01550.0295-0.042-0.09360.06680.05960.1023-00.92980.093-0.2970.6027-0.30270.849310.8888-15.2407-29.2931
170.35650.29040.03350.22830.07950.33370.11510.383-0.0611-0.03960.04320.26320.1782-0.01480.28340.37090.0282-0.16420.2886-0.19210.270714.701812.165-20.2271
180.00160.0017-0.00630.0045-0.0014-0.00030.04680.0039-0.19630.0372-0.0814-0.06560.14720.0883-01.626-0.0919-0.32230.6206-0.14391.260713.8239-31.6464-22.0632
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 285 )
3X-RAY DIFFRACTION3chain 'A' and (resid 286 through 325 )
4X-RAY DIFFRACTION4chain 'B' and (resid 335 through 408 )
5X-RAY DIFFRACTION5chain 'B' and (resid 409 through 509 )
6X-RAY DIFFRACTION6chain 'C' and (resid 4 through 119 )
7X-RAY DIFFRACTION7chain 'C' and (resid 120 through 270 )
8X-RAY DIFFRACTION8chain 'C' and (resid 271 through 325 )
9X-RAY DIFFRACTION9chain 'D' and (resid 335 through 356 )
10X-RAY DIFFRACTION10chain 'D' and (resid 357 through 466 )
11X-RAY DIFFRACTION11chain 'D' and (resid 467 through 492 )
12X-RAY DIFFRACTION12chain 'D' and (resid 493 through 509 )
13X-RAY DIFFRACTION13chain 'E' and (resid 4 through 96 )
14X-RAY DIFFRACTION14chain 'E' and (resid 97 through 270 )
15X-RAY DIFFRACTION15chain 'E' and (resid 271 through 325 )
16X-RAY DIFFRACTION16chain 'F' and (resid 335 through 371 )
17X-RAY DIFFRACTION17chain 'F' and (resid 372 through 466 )
18X-RAY DIFFRACTION18chain 'F' and (resid 467 through 509 )

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