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- PDB-4mhi: Crystal structure of a H5N1 influenza virus hemagglutinin from A/... -

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Basic information

Entry
Database: PDB / ID: 4mhi
TitleCrystal structure of a H5N1 influenza virus hemagglutinin from A/goose/Guangdong/1/96
Components(Hemagglutinin ...) x 2
KeywordsVIRAL PROTEIN / H5N1 influenza virus / epitope / glycoprotein / progenitor
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
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.595 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: J.Virol. / Year: 2013
Title: A Unique and Conserved Neutralization Epitope in H5N1 Influenza Viruses Identified by an Antibody against the A/Goose/Guangdong/1/96 Hemagglutinin.
Authors: Zhu, X. / Guo, Y.H. / Jiang, T. / Wang, Y.D. / Chan, K.H. / Li, X.F. / Yu, W. / McBride, R. / Paulson, J.C. / Yuen, K.Y. / Qin, C.F. / Che, X.Y. / Wilson, I.A.
History
DepositionAug 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
G: Hemagglutinin HA1 chain
H: Hemagglutinin HA2 chain
I: Hemagglutinin HA1 chain
J: Hemagglutinin HA2 chain
K: Hemagglutinin HA1 chain
L: Hemagglutinin HA2 chain
M: Hemagglutinin HA1 chain
N: Hemagglutinin HA2 chain
O: Hemagglutinin HA1 chain
P: Hemagglutinin HA2 chain
Q: Hemagglutinin HA1 chain
R: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)535,01540
Polymers528,36018
Non-polymers6,65422
Water2,108117
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,27813
Polymers176,1206
Non-polymers2,1587
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31970 Å2
ΔGint-87 kcal/mol
Surface area61920 Å2
MethodPISA
2
G: Hemagglutinin HA1 chain
H: Hemagglutinin HA2 chain
I: Hemagglutinin HA1 chain
J: Hemagglutinin HA2 chain
K: Hemagglutinin HA1 chain
L: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,07513
Polymers176,1206
Non-polymers1,9557
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30900 Å2
ΔGint-98 kcal/mol
Surface area61440 Å2
MethodPISA
3
M: Hemagglutinin HA1 chain
N: Hemagglutinin HA2 chain
O: Hemagglutinin HA1 chain
P: Hemagglutinin HA2 chain
Q: Hemagglutinin HA1 chain
R: Hemagglutinin HA2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,66214
Polymers176,1206
Non-polymers2,5418
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31640 Å2
ΔGint-97 kcal/mol
Surface area61770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.482, 225.728, 211.633
Angle α, β, γ (deg.)90.00, 98.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Hemagglutinin ... , 2 types, 18 molecules ACEGIKMOQBDFHJLNPR

#1: Protein
Hemagglutinin HA1 chain


Mass: 37812.707 Da / Num. of mol.: 9 / Fragment: receptor binding domain (UNP residues 17-346)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd / Gene: HA / Plasmid: pfastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q9Q0U6
#2: Protein
Hemagglutinin HA2 chain


Mass: 20894.012 Da / Num. of mol.: 9 / Fragment: membrane fusion domain (UNP residues 347-521)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Goose/Guangdong/1/1996 H5N1 genotype Gs/Gd / Gene: HA / Plasmid: pfastbac-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: Q9Q0U6

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Sugars , 3 types, 22 molecules

#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.: 7
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
#4: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 14
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 , 1 types, 117 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.24 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.1 M Tris, pH 8.2, 21% MPEG2000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 15, 2010
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.595→50 Å / Num. obs: 196526 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Rsym value: 0.1 / Net I/σ(I): 22.8
Reflection shellResolution: 2.595→2.69 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.7 / % possible all: 75.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GBM

3gbm


Resolution: 2.595→49.657 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 9845 5.02 %RANDOM
Rwork0.1893 ---
obs0.192 195939 94.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.595→49.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35586 0 431 117 36134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00937269
X-RAY DIFFRACTIONf_angle_d1.3150475
X-RAY DIFFRACTIONf_dihedral_angle_d16.87713941
X-RAY DIFFRACTIONf_chiral_restr0.0765460
X-RAY DIFFRACTIONf_plane_restr0.0066569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.595-2.62460.37922320.35674188X-RAY DIFFRACTION65
2.6246-2.65550.42582550.37754911X-RAY DIFFRACTION75
2.6555-2.68780.44992720.39885099X-RAY DIFFRACTION77
2.6878-2.72190.38762570.32375141X-RAY DIFFRACTION79
2.7219-2.75770.39322700.31725438X-RAY DIFFRACTION83
2.7577-2.79550.38643260.31985867X-RAY DIFFRACTION90
2.7955-2.83540.36133140.29575823X-RAY DIFFRACTION91
2.8354-2.87770.38053190.2846294X-RAY DIFFRACTION95
2.8777-2.92270.35163120.28696423X-RAY DIFFRACTION98
2.9227-2.97060.35223530.28526394X-RAY DIFFRACTION99
2.9706-3.02180.33443470.28076553X-RAY DIFFRACTION100
3.0218-3.07670.33883430.25786470X-RAY DIFFRACTION100
3.0767-3.13590.30133660.2546506X-RAY DIFFRACTION100
3.1359-3.19990.33893910.25486488X-RAY DIFFRACTION100
3.1999-3.26950.31633110.25176550X-RAY DIFFRACTION100
3.2695-3.34550.28933340.24086532X-RAY DIFFRACTION100
3.3455-3.42920.32273310.2546572X-RAY DIFFRACTION100
3.4292-3.52180.2883140.2426548X-RAY DIFFRACTION100
3.5218-3.62540.2863850.20656513X-RAY DIFFRACTION100
3.6254-3.74240.26583410.19596485X-RAY DIFFRACTION100
3.7424-3.87610.23253530.18916530X-RAY DIFFRACTION100
3.8761-4.03130.22983620.16736556X-RAY DIFFRACTION100
4.0313-4.21460.21053170.14896499X-RAY DIFFRACTION100
4.2146-4.43670.16283480.13056503X-RAY DIFFRACTION100
4.4367-4.71450.18083480.13336545X-RAY DIFFRACTION99
4.7145-5.07820.19973370.13646549X-RAY DIFFRACTION100
5.0782-5.58860.19213670.14266554X-RAY DIFFRACTION100
5.5886-6.39580.20793640.15776518X-RAY DIFFRACTION100
6.3958-8.05250.22493380.1616619X-RAY DIFFRACTION100
8.0525-49.66590.1893380.16146426X-RAY DIFFRACTION97
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)
10.2071-1.1913-0.29076.3330.53790.3690.0110.0613-0.1506-0.96810.12340.7332-0.0756-0.143-0.13070.5863-0.0379-0.15550.650.04780.6213-18.9174-22.628477.0134
20.46150.69830.15023.49820.5290.2158-0.05970.0025-0.0528-0.3179-0.00970.35860.2484-0.02290.05950.7523-0.10690.10250.5648-0.01480.61-7.8235-74.43180.1522
30.0285-0.64680.00993.1666-0.08770.4007-0.0622-0.07090.1855-0.23290.1221-1.54-0.08630.1375-0.04150.5066-0.05680.05760.7467-0.10151.365215.8473-19.684583.4033
40.7024-0.9885-0.23823.34170.67740.7529-0.1276-0.0511-0.0104-0.09760.2172-0.81480.25350.1677-0.10230.67760.03660.05080.6248-0.06810.830312.6617-72.67682.1885
50.7324-0.4129-0.34963.85150.75410.4071-0.2306-0.15710.15911.15150.3534-0.20580.2269-0.0128-0.10140.95910.2283-0.1020.7926-0.02910.4992-6.5887-23.6358110.3975
61.1739-0.21950.31532.72050.03421.0749-0.1735-0.1313-0.53471.09770.2486-0.20690.70490.0172-0.07431.06270.07620.06330.63360.06110.72110.6568-74.833898.876
70.5437-0.3662-0.19173.23810.63970.2757-0.058-0.1063-0.08190.5561-0.00640.00060.1938-0.04270.06350.80330.05540.01830.7466-0.07230.5293.702-24.1007180.2374
81.288-1.1842-0.15332.2835-0.28131.2042-0.1968-0.112-0.63450.9113-0.01760.35330.43460.10270.19561.0150.06970.0240.62760.06130.909212.5143-75.2135169.4049
90.3995-0.4170.02173.22070.65720.55660.09660.08290.0085-0.6131-0.0701-0.0497-0.223-0.0917-0.02030.66350.09710.03450.6205-0.01770.3903-4.243-22.9626145.6209
100.3730.29110.06163.21180.69540.72040.03030.06-0.23180.0591-0.11030.12840.237-0.0680.10870.635-0.00030.04420.6531-0.12930.76756.1306-74.7235149.7214
110.4019-0.0844-0.09842.47610.0810.52840.0187-0.0444-0.0064-0.1690.1317-0.9228-0.09550.1906-0.13290.5905-0.05840.02430.7258-0.13230.977129.4338-19.9182156.4171
120.93170.2336-0.49012.25970.05781.043-0.1073-0.0536-0.4647-0.5504-0.0359-0.82950.40290.17040.12330.80870.14990.0280.6683-0.06161.053826.326-72.9276154.4053
13-0.1682-0.156-0.01282.555-0.05670.01230.0628-0.06730.05870.1268-0.1739-1.3963-0.07890.14930.08690.6898-0.2122-0.10240.93160.12981.410643.4018-21.769225.609
140.962-0.5031-0.2742.61420.71981.1476-0.03790.0029-0.1343-0.2273-0.0764-0.70470.06430.28570.10560.5912-0.01520.04010.74940.13380.890837.7918-74.4502221.152
150.27960.2014-0.25172.89220.23860.23710.1716-0.27050.03820.7134-0.1743-0.3347-0.1524-0.05250.01651.1597-0.1258-0.18620.8787-0.01070.590218.9556-26.0052250.8788
160.9031-0.07980.07293.12860.030.80270.0294-0.1235-0.2860.8217-0.1574-0.45220.23970.07580.12550.7934-0.0744-0.06040.72730.12690.672724.843-76.7489236.6724
170.1386-0.6215-0.00634.62810.27310.39060.0198-0.0235-0.0164-0.6118-0.0280.0431-0.1856-0.0780.01490.75330.002-0.03440.67980.04440.49379.1314-22.5197216.7956
180.45290.58930.14483.35840.43730.60440.00270.04730.0462-0.2402-0.0530.04540.1230.07520.05430.666-0.05490.02680.68410.06960.58517.3981-74.9136217.6217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 324 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 173 )
3X-RAY DIFFRACTION3chain 'C' and (resid 9 through 324 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 173 )
5X-RAY DIFFRACTION5chain 'E' and (resid 9 through 324 )
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 173 )
7X-RAY DIFFRACTION7chain 'G' and (resid 9 through 324 )
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 173 )
9X-RAY DIFFRACTION9chain 'I' and (resid 9 through 324 )
10X-RAY DIFFRACTION10chain 'J' and (resid 1 through 173 )
11X-RAY DIFFRACTION11chain 'K' and (resid 9 through 324 )
12X-RAY DIFFRACTION12chain 'L' and (resid 1 through 173 )
13X-RAY DIFFRACTION13chain 'M' and (resid 9 through 324 )
14X-RAY DIFFRACTION14chain 'N' and (resid 1 through 173 )
15X-RAY DIFFRACTION15chain 'O' and (resid 9 through 324 )
16X-RAY DIFFRACTION16chain 'P' and (resid 1 through 173 )
17X-RAY DIFFRACTION17chain 'Q' and (resid 9 through 324 )
18X-RAY DIFFRACTION18chain 'R' and (resid 1 through 173 )

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  • 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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