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- PDB-3lzf: Crystal Structure of Fab 2D1 in Complex with the 1918 Influenza V... -

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Basic information

Entry
Database: PDB / ID: 3lzf
TitleCrystal Structure of Fab 2D1 in Complex with the 1918 Influenza Virus Hemagglutinin
Components
  • (Hemagglutinin, ...) x 2
  • 2D1 Fab, Heavy Chain
  • 2D1 Fab, Light Chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / hemagglutinin / Fab / neutralizing antibodies / antibody / pandemic flu / swine flu / Envelope protein / Fusion protein / Glycoprotein / antigen / Virion / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsEkiert, D.C. / Wilson, I.A.
CitationJournal: Science / Year: 2010
Title: Structural basis of preexisting immunity to the 2009 H1N1 pandemic influenza virus.
Authors: Xu, R. / Ekiert, D.C. / Krause, J.C. / Hai, R. / Crowe, J.E. / Wilson, I.A.
History
DepositionMar 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
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_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_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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 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, HA1 Subunit
B: Hemagglutinin, HA2 Subunit
H: 2D1 Fab, Heavy Chain
L: 2D1 Fab, Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1788
Polymers104,3594
Non-polymers1,8194
Water00
1
A: Hemagglutinin, HA1 Subunit
B: Hemagglutinin, HA2 Subunit
H: 2D1 Fab, Heavy Chain
L: 2D1 Fab, Light Chain
hetero molecules

A: Hemagglutinin, HA1 Subunit
B: Hemagglutinin, HA2 Subunit
H: 2D1 Fab, Heavy Chain
L: 2D1 Fab, Light Chain
hetero molecules

A: Hemagglutinin, HA1 Subunit
B: Hemagglutinin, HA2 Subunit
H: 2D1 Fab, Heavy Chain
L: 2D1 Fab, Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,53424
Polymers313,07812
Non-polymers5,45612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
2
A: Hemagglutinin, HA1 Subunit
B: Hemagglutinin, HA2 Subunit
hetero molecules

A: Hemagglutinin, HA1 Subunit
B: Hemagglutinin, HA2 Subunit
hetero molecules

A: Hemagglutinin, HA1 Subunit
B: Hemagglutinin, HA2 Subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,99818
Polymers170,5426
Non-polymers5,45612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area28120 Å2
ΔGint-147 kcal/mol
Surface area60120 Å2
MethodPISA
3
H: 2D1 Fab, Heavy Chain
L: 2D1 Fab, Light Chain


Theoretical massNumber of molelcules
Total (without water)47,5122
Polymers47,5122
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-25 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.745, 161.745, 143.473
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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Hemagglutinin, ... , 2 types, 2 molecules AB

#1: Protein Hemagglutinin, HA1 Subunit / Hemagglutinin HA1 chain / Hemagglutinin HA2 chain


Mass: 36452.797 Da / Num. of mol.: 1 / Fragment: Ectodomain HA1, residues 18-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/South Carolina/1/1918(H1N1) / Gene: HA, Hemagglutinin / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): BTI-TN-5B1-4 / References: UniProt: Q9WFX3
#2: Protein Hemagglutinin, HA2 Subunit / Hemagglutinin HA1 chain / Hemagglutinin HA2 chain


Mass: 20394.445 Da / Num. of mol.: 1 / Fragment: Ectodomain HA2, residues 345-520
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/South Carolina/1/1918(H1N1) / Gene: HA, Hemagglutinin / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): BTI-TN-5B1-4 / References: UniProt: Q9WFX3

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Antibody , 2 types, 2 molecules HL

#3: Antibody 2D1 Fab, Heavy Chain


Mass: 24699.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Immunoglobulin, Gamma Chain / Plasmid: pEE6.4 / Cell line (production host): HEK 293F / Organ (production host): kidney / Production host: Homo sapiens (human)
#4: Antibody 2D1 Fab, Light Chain


Mass: 22812.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Immunoglobulin, Lambda Chain / Plasmid: pEE12.4 / Cell line (production host): HEK 293F / Organ (production host): kidney / Production host: Homo sapiens (human)

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Sugars , 3 types, 4 molecules

#5: 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.: 2
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
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: 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.: 1
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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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: 5.19 Å3/Da / Density % sol: 76.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 16% PEG1000, 100mM PIPES pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0333 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 54245 / Num. obs: 53366 / % possible obs: 98.4 % / Observed criterion σ(I): 1 / Redundancy: 10.3 % / Biso Wilson estimate: 90.4 Å2 / Rsym value: 0.04
Reflection shellResolution: 2.8→2.89 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.49

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.4.0069refinement
HKL-2000data reduction
XPREPdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49.69 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.919 / SU B: 28.678 / SU ML: 0.251 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2591 2596 4.9 %RANDOM
Rwork0.2301 ---
obs0.23154 50122 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.287 Å2
Baniso -1Baniso -2Baniso -3
1-2.96 Å21.48 Å20 Å2
2--2.96 Å20 Å2
3----4.44 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7087 0 120 0 7207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227401
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.96710097
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.855921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.64524.801302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.626151160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3911526
X-RAY DIFFRACTIONr_chiral_restr0.1080.21150
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215560
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6291.54597
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21927434
X-RAY DIFFRACTIONr_scbond_it1.99232804
X-RAY DIFFRACTIONr_scangle_it3.3844.52662
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 189 -
Rwork0.414 3230 -
obs--87.46 %
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)
12.10810.6513-3.39931.1235-1.91377.15370.1842-0.07620.0502-0.1275-0.3008-0.0084-0.30380.32710.1166-0.498-0.12070.0344-0.36760.0579-0.278661.0598-41.261646.3841
22.0350.42523.06251.44880.092212.23890.0950.9820.2094-1.18470.07780.43020.3235-0.6564-0.17290.51120.1052-0.26470.50420.1551-0.296768.7448-44.1739-6.4675
36.21354.3923-4.29676.0701-4.8837.32861.2646-1.9979-0.65021.8344-1.4953-0.528-1.03081.3520.2307-0.0812-0.554-0.23350.48170.2715-0.235341.096-62.8934100.1929
42.27183.2345-1.97818.2461-6.02319.96480.2035-1.5609-1.8410.3829-1.4413-1.78971.53361.11531.2377-0.1105-0.0982-0.16360.71660.9970.793247.7756-79.490297.3284
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 325
2X-RAY DIFFRACTION2B1 - 173
3X-RAY DIFFRACTION3H2 - 223
4X-RAY DIFFRACTION4L2 - 211

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