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- PDB-4kw1: Structure of a/egypt/n03072/2010 h5 ha -

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Basic information

Entry
Database: PDB / ID: 4kw1
TitleStructure of a/egypt/n03072/2010 h5 ha
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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
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: 2.5 Å
AuthorsShore, D.A. / Yang, H. / Carney, P.J. / Chang, J.C. / Stevens, J.
CitationJournal: Plos One / Year: 2013
Title: Structural and antigenic variation among diverse clade 2 H5N1 viruses.
Authors: Shore, D.A. / Yang, H. / Balish, A.L. / Shepard, S.S. / Carney, P.J. / Chang, J.C. / Davis, C.T. / Donis, R.O. / Villanueva, J.M. / Klimov, A.I. / Stevens, J.
History
DepositionMay 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: 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 / 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_struct_special_symmetry / 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.occupancy / _atom_site.type_symbol / _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_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
G: Hemagglutinin
H: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,98028
Polymers231,9678
Non-polymers6,01320
Water1,35175
1
A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,21521
Polymers173,9756
Non-polymers5,23915
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area36420 Å2
ΔGint-112 kcal/mol
Surface area61930 Å2
MethodPISA
2
C: Hemagglutinin
D: Hemagglutinin
hetero molecules

C: Hemagglutinin
D: Hemagglutinin
hetero molecules

C: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,21521
Polymers173,9756
Non-polymers5,23915
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area35130 Å2
ΔGint-97 kcal/mol
Surface area60040 Å2
MethodPISA
3
E: Hemagglutinin
F: Hemagglutinin
hetero molecules

E: Hemagglutinin
F: Hemagglutinin
hetero molecules

E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,75521
Polymers173,9756
Non-polymers3,78015
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area34450 Å2
ΔGint-104 kcal/mol
Surface area59560 Å2
MethodPISA
4
G: Hemagglutinin
H: Hemagglutinin
hetero molecules

G: Hemagglutinin
H: Hemagglutinin
hetero molecules

G: Hemagglutinin
H: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,75521
Polymers173,9756
Non-polymers3,78015
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area34180 Å2
ΔGint-113 kcal/mol
Surface area59010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.066, 98.066, 655.022
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-201-

PO4

21B-201-

PO4

31D-201-

PO4

41D-302-

HOH

51D-309-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14B
24D
15B
25F
16B
26H
17C
27E
18C
28G
19D
29F
110D
210H
111E
211G
112F
212H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 320
2010C1 - 320
1020A1 - 320
2020E1 - 320
1030A1 - 320
2030G1 - 320
1040B11 - 174
2040D11 - 174
1050B11 - 175
2050F11 - 175
1060B12 - 174
2060H12 - 174
1070C1 - 320
2070E1 - 320
1080C1 - 320
2080G1 - 320
1090D10 - 173
2090F10 - 173
10100D12 - 174
20100H12 - 174
10110E1 - 320
20110G1 - 320
10120F12 - 176
20120H12 - 176

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Hemagglutinin /


Mass: 37082.715 Da / Num. of mol.: 4 / Fragment: HA1 residues 17-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus
Strain: A/reassortant/IDCDC_RG29(Egypt/N03072/2010 x Puerto Rico/8/1934)(H5N1)
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G1JUF7
#2: Protein
Hemagglutinin /


Mass: 20909.117 Da / Num. of mol.: 4 / Fragment: HA2 residues 342-401
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus
Strain: A/reassortant/IDCDC_RG29(Egypt/N03072/2010 x Puerto Rico/8/1934)(H5N1)
Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: G1JUF7

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Sugars , 3 types, 12 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#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.: 6
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-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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, 83 molecules

#6: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.93 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 25% PEG 3350, 100mM Tris-HCl pH8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2011
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.893
11K, H, -L20.107
ReflectionResolution: 2.5→50 Å / Num. obs: 81024 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rsym value: 0.076
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.1 % / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→44.73 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.984 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 4025 5 %RANDOM
Rwork0.193 ---
obs0.194 76734 99.6 %-
all-79907 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.84 Å2
Baniso -1Baniso -2Baniso -3
1--4.33 Å20 Å20 Å2
2---4.33 Å20 Å2
3---8.67 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15234 0 386 75 15695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01915986
X-RAY DIFFRACTIONr_bond_other_d0.0090.0214696
X-RAY DIFFRACTIONr_angle_refined_deg1.8861.96321677
X-RAY DIFFRACTIONr_angle_other_deg1.4993.00333703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.61251887
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.70525.165817
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.434152718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5521581
X-RAY DIFFRACTIONr_chiral_restr0.1080.22369
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218096
X-RAY DIFFRACTIONr_gen_planes_other0.0070.023734
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A174990.15
12C174990.15
21A166190.16
22E166190.16
31A171650.15
32G171650.15
41B74740.17
42D74740.17
51B73920.18
52F73920.18
61B81980.14
62H81980.14
71C168610.14
72E168610.14
81C169780.16
82G169780.16
91D75460.17
92F75460.17
101D74490.16
102H74490.16
111E164650.16
112G164650.16
121F73830.17
122H73830.17
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 300 -
Rwork0.161 5579 -
obs--98.46 %
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)
10.12280.00360.16980.0902-0.04271.07130.0301-0.0264-0.01440.02960.01110.03050.1191-0.1806-0.04120.0294-0.01820.00830.0329-0.00610.15331.854818.7764-92.5643
20.25880.03850.84310.47790.70915.08790.0848-0.0245-0.01790.0732-0.0642-0.01780.6193-0.1012-0.02060.08150.0061-0.00010.1176-0.02640.17438.332823.8033-144.9397
30.08810.0333-0.06280.09060.05910.6432-0.02210.0093-0.01350.02490.0228-0.02340.1630.0615-0.00070.06370.0125-0.00040.01210.00110.13120.156137.2575-93.5842
40.23180.1027-0.10.5719-1.08354.1425-0.0690.0214-0.09260.01630.0811-0.01050.1179-0.2561-0.01210.08340.03070.01930.06350.02220.18981.182445.0314-42.2609
50.0772-0.0221-0.10610.018-0.09041.5316-0.0206-0.0312-0.0130.01120.03150.0166-0.0586-0.2536-0.01090.07490.03680.01060.0925-0.0050.125632.452137.7672-15.7424
60.346-0.1965-0.83790.65860.30972.82050.0576-0.0890.0174-0.0417-0.08970.093-0.44160.23950.03220.1533-0.00920.01630.2967-0.00950.211738.381332.805535.0319
70.1050.03480.03960.12080.00211.697-0.0309-0.0074-0.0002-0.02390.02430.0002-0.2450.03410.00660.1262-0.0027-0.01170.00820.00340.12520.335119.184448.023
80.5201-0.18820.64050.6126-2.016.73670.019-0.02950.00760.03450.07260.0738-0.1444-0.2546-0.09160.191-0.0734-0.06210.04660.00730.1761.561111.4285-3.7876
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 321
2X-RAY DIFFRACTION1A401 - 408
3X-RAY DIFFRACTION2B11 - 175
4X-RAY DIFFRACTION3C1 - 320
5X-RAY DIFFRACTION3C401 - 408
6X-RAY DIFFRACTION4D10 - 174
7X-RAY DIFFRACTION5E1 - 320
8X-RAY DIFFRACTION5E401 - 405
9X-RAY DIFFRACTION6F10 - 176
10X-RAY DIFFRACTION7G1 - 320
11X-RAY DIFFRACTION7G401 - 405
12X-RAY DIFFRACTION8H12 - 176

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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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