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- PDB-4ln4: The crystal structure of hemagglutinin form a h7n9 influenza viru... -

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Basic information

Entry
Database: PDB / ID: 4ln4
TitleThe crystal structure of hemagglutinin form a h7n9 influenza virus (a/shanghai/1/2013) in complex with lstb
Components(Hemagglutinin) x 2
KeywordsVIRAL PROTEIN / RECEPTOR SPECIFICITY
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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsYang, H. / Carney, P.J. / Chang, J.C. / Villanueva, J.M. / Stevens, J.
CitationJournal: J.Virol. / Year: 2013
Title: Structural Analysis of the Hemagglutinin from the Recent 2013 H7N9 Influenza Virus.
Authors: Yang, H. / Carney, P.J. / Chang, J.C. / Villanueva, J.M. / Stevens, J.
History
DepositionJul 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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.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 / _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.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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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_comp_id
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
I: Hemagglutinin
J: Hemagglutinin
K: Hemagglutinin
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)341,92527
Polymers337,51112
Non-polymers4,41415
Water0
1
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Hemagglutinin
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,84215
Polymers168,7556
Non-polymers3,0879
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33890 Å2
ΔGint-104 kcal/mol
Surface area58220 Å2
MethodPISA
2
A: Hemagglutinin
B: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2815
Polymers56,2522
Non-polymers1,0293
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-19 kcal/mol
Surface area23740 Å2
MethodPISA
3
C: Hemagglutinin
D: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2815
Polymers56,2522
Non-polymers1,0293
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-20 kcal/mol
Surface area23780 Å2
MethodPISA
4
E: Hemagglutinin
F: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2815
Polymers56,2522
Non-polymers1,0293
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-20 kcal/mol
Surface area23860 Å2
MethodPISA
5
G: Hemagglutinin
H: Hemagglutinin
hetero molecules

I: Hemagglutinin
J: Hemagglutinin
hetero molecules

K: Hemagglutinin
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,08312
Polymers168,7556
Non-polymers1,3276
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area32210 Å2
ΔGint-128 kcal/mol
Surface area56160 Å2
MethodPISA
6
G: Hemagglutinin
H: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6944
Polymers56,2522
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-27 kcal/mol
Surface area22950 Å2
MethodPISA
7
I: Hemagglutinin
J: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6944
Polymers56,2522
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-27 kcal/mol
Surface area22960 Å2
MethodPISA
8
K: Hemagglutinin
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6944
Polymers56,2522
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-26 kcal/mol
Surface area22940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.006, 153.959, 153.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14A
24I
15A
25K
16B
26D
17B
27F
18B
28H
19B
29J
110B
210L
111C
211E
112C
212G
113C
213I
114C
214K
115D
215F
116D
216H
117D
217J
118D
218L
119E
219G
120E
220I
121E
221K
122F
222H
123F
223J
124F
224L
125G
225I
126G
226K
127H
227J
128H
228L
129I
229K
130J
230L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A0 - 315
2010C0 - 315
1020A0 - 315
2020E0 - 315
1030A0 - 315
2030G0 - 315
1040A0 - 315
2040I0 - 315
1050A0 - 315
2050K0 - 315
1060B5 - 171
2060D5 - 171
1070B5 - 171
2070F5 - 171
1080B6 - 168
2080H6 - 168
1090B6 - 168
2090J6 - 168
10100B6 - 168
20100L6 - 168
10110C0 - 315
20110E0 - 315
10120C0 - 315
20120G0 - 315
10130C0 - 315
20130I0 - 315
10140C0 - 315
20140K0 - 315
10150D5 - 171
20150F5 - 171
10160D6 - 168
20160H6 - 168
10170D6 - 168
20170J6 - 168
10180D6 - 168
20180L6 - 168
10190E0 - 315
20190G0 - 315
10200E0 - 315
20200I0 - 315
10210E0 - 315
20210K0 - 315
10220F6 - 168
20220H6 - 168
10230F6 - 168
20230J6 - 168
10240F6 - 168
20240L6 - 168
10250G0 - 315
20250I0 - 315
10260G0 - 315
20260K0 - 315
10270H6 - 169
20270J6 - 169
10280H6 - 169
20280L6 - 169
10290I0 - 315
20290K0 - 315
10300J6 - 169
20300L6 - 169

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30

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Components

#1: Protein
Hemagglutinin /


Mass: 35379.805 Da / Num. of mol.: 6 / Fragment: HA1 subunit residues 19-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/02/2013(H7N9) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R4NN21*PLUS
#2: Protein
Hemagglutinin /


Mass: 20871.959 Da / Num. of mol.: 6 / Fragment: HA2 subunit residues 340-517
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Shanghai/02/2013(H7N9) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: R4NN21*PLUS
#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.: 3
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: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.38 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 8.5
Details: 0.2M MgCl2, 0.1M Tris-HCl pH8.5, 16% PEG4000, Microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 3, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 5003 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.1→3.18 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→48.75 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.922 / SU B: 45.769 / SU ML: 0.344 / Cross valid method: THROUGHOUT / σ(F): 1.8 / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 3371 5.1 %RANDOM
Rwork0.20099 ---
all0.21 66487 --
obs0.20294 63160 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 100.765 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--2.49 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22542 0 285 0 22827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01923292
X-RAY DIFFRACTIONr_bond_other_d0.0040.0221519
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.95131485
X-RAY DIFFRACTIONr_angle_other_deg0.9583.00349302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.03552877
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32224.5741161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.645153951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.89215165
X-RAY DIFFRACTIONr_chiral_restr0.0780.23420
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0226895
X-RAY DIFFRACTIONr_gen_planes_other0.0040.025532
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A185810.05
12C185810.05
21A187140.03
22E187140.03
31A186580.04
32G186580.04
41A186440.05
42I186440.05
51A186330.04
52K186330.04
61B91040.05
62D91040.05
71B91470.05
72F91470.05
81B88290.05
82H88290.05
91B88510.05
92J88510.05
101B88230.06
102L88230.06
111C186790.04
112E186790.04
121C186170.04
122G186170.04
131C186360.05
132I186360.05
141C186890.04
142K186890.04
151D91440.04
152F91440.04
161D88490.04
162H88490.04
171D88710.04
172J88710.04
181D88420.05
182L88420.05
191E187140.03
192G187140.03
201E187120.04
202I187120.04
211E187120.03
212K187120.03
221F88700.04
222H88700.04
231F88720.04
232J88720.04
241F88420.05
242L88420.05
251G188300.03
252I188300.03
261G187640.03
262K187640.03
271H90370.02
272J90370.02
281H90100.03
282L90100.03
291I187490.04
292K187490.04
301J90270.03
302L90270.03
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 250 -
Rwork0.33 4457 -
obs--97.23 %
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)
10.821-0.7233-0.59390.86630.9221.4322-0.13750.2521-0.19780.2728-0.15650.20780.2719-0.06680.2940.221-0.10480.04870.1838-0.10610.229257.6679-6.51992.0136
21.177-0.538-0.70730.33440.35271.00140.09830.06580.05640.0665-0.0342-0.01870.0798-0.2859-0.06410.1933-0.06980.07820.1658-0.0740.207634.70124.596833.6758
30.9698-0.9486-0.77981.36170.62450.8561-0.1585-0.2050.28780.08030.2784-0.29740.28010.1716-0.11990.23280.0553-0.11980.0625-0.06350.318783.51812.025419.3229
40.6135-0.5474-0.89051.12090.92231.6096-0.04970.05030.11390.3219-0.0351-0.13940.077-0.10840.08480.23410.0609-0.09580.058-0.06470.294152.391833.733942.2316
51.3829-0.675-0.88310.8740.75830.86590.27630.28610.1151-0.1814-0.1421-0.2781-0.1999-0.2399-0.13430.10590.05880.09130.16540.12160.348874.981619.3767-6.499
60.992-0.7104-0.32521.26040.570.4444-0.00360.15320.3490.10060.0445-0.10930.0267-0.1198-0.04080.11480.0680.08420.16830.09190.351643.24942.275624.5672
70.1631-0.19870.16960.9988-0.25240.4852-0.1055-0.0117-0.04660.16750.1638-0.0469-0.0643-0.1549-0.05830.16110.0203-0.09130.1164-0.00940.230897.857633.994944.1229
81.0056-0.57030.46140.6213-0.41320.29090.0770.08920.1416-0.1191-0.0994-0.00750.06310.04710.02240.22940.1362-0.17560.19710.03350.32174.693766.866214.9758
90.55750.16910.23580.17190.17140.7892-0.0593-0.05820.1845-0.0159-0.10560.01960.0665-0.15150.1650.1586-0.0886-0.01320.1247-0.01690.231232.7785-20.853833.8939
100.32120.55090.46341.07580.6730.78350.00420.0783-0.07790.09290.1266-0.1247-0.06020.1145-0.13090.2874-0.1519-0.03770.202-0.14530.294261.9982.32166.6614
110.77910.2446-0.16360.5827-0.27350.2070.17520.04930.1880.1772-0.06080.0571-0.03080.0296-0.11440.1549-0.01260.02410.11590.07090.226242.970444.2103-20.7763
120.38450.3211-0.46290.3538-0.45290.9895-0.1419-0.0136-0.1448-0.07940.0096-0.12690.1522-0.12750.13230.1952-0.02980.13120.27240.18060.281910.094214.99242.306
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 315
2X-RAY DIFFRACTION1A401 - 404
3X-RAY DIFFRACTION2B5 - 171
4X-RAY DIFFRACTION2B500
5X-RAY DIFFRACTION3C0 - 315
6X-RAY DIFFRACTION3C401 - 404
7X-RAY DIFFRACTION4D5 - 171
8X-RAY DIFFRACTION4D500
9X-RAY DIFFRACTION5E0 - 315
10X-RAY DIFFRACTION5E401 - 404
11X-RAY DIFFRACTION6F5 - 171
12X-RAY DIFFRACTION6F500
13X-RAY DIFFRACTION7G0 - 315
14X-RAY DIFFRACTION7G800
15X-RAY DIFFRACTION8H6 - 169
16X-RAY DIFFRACTION8H500
17X-RAY DIFFRACTION9I0 - 315
18X-RAY DIFFRACTION9I800
19X-RAY DIFFRACTION10J6 - 169
20X-RAY DIFFRACTION10J500
21X-RAY DIFFRACTION11K0 - 315
22X-RAY DIFFRACTION11K800
23X-RAY DIFFRACTION12L6 - 169
24X-RAY DIFFRACTION12L500

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