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- PDB-3gbn: Crystal Structure of Fab CR6261 in Complex with the 1918 H1N1 inf... -

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Basic information

Entry
Database: PDB / ID: 3gbn
TitleCrystal Structure of Fab CR6261 in Complex with the 1918 H1N1 influenza virus hemagglutinin
Components
  • (Hemagglutinin) x 2
  • Fab Heavy Chain
  • Fab Lambda Light Chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / hemagglutinin / Fab / neutralizing antibodies / antibody / pandemic flu / Cell membrane / Envelope protein / Fusion protein / Glycoprotein / Lipoprotein / Membrane / Palmitate / Transmembrane / 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
2-ETHOXYETHANOL / Unknown ligand / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEkiert, D.C. / Elsliger, M.A. / Wilson, I.A.
CitationJournal: Science / Year: 2009
Title: Antibody recognition of a highly conserved influenza virus epitope.
Authors: Ekiert, D.C. / Bhabha, G. / Elsliger, M.A. / Friesen, R.H. / Jongeneelen, M. / Throsby, M. / Goudsmit, J. / Wilson, I.A.
History
DepositionFeb 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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 / 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.auth_asym_id / _atom_site.label_asym_id ..._atom_site.auth_asym_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
H: Fab Heavy Chain
L: Fab Lambda Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,89717
Polymers104,0864
Non-polymers1,81113
Water5,278293
1
A: Hemagglutinin
B: Hemagglutinin
H: Fab Heavy Chain
L: Fab Lambda Light Chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: Fab Heavy Chain
L: Fab Lambda Light Chain
hetero molecules

A: Hemagglutinin
B: Hemagglutinin
H: Fab Heavy Chain
L: Fab Lambda Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,69251
Polymers312,25812
Non-polymers5,43439
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area52610 Å2
ΔGint-197 kcal/mol
Surface area104050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.918, 202.249, 202.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11B-237-

HOH

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 36452.797 Da / Num. of mol.: 1 / Fragment: Receptor binding domain, HA1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Strain: A/South Carolina/1/1918 / Gene: HA, Hemagglutinin (HA) / Plasmid: pFASTBAC-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): HI5 / References: UniProt: Q9WFX3
#2: Protein Hemagglutinin / Hemagglutinin HA1 chain / Hemagglutinin HA2 chain


Mass: 20394.445 Da / Num. of mol.: 1 / Fragment: Membrane Fusion domain, HA2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Strain: A/South Carolina/1/1918 / Gene: HA, Hemagglutinin (HA) / Plasmid: pFASTBAC-HT / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): HI5 / References: UniProt: Q9WFX3

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Antibody , 2 types, 2 molecules HL

#3: Antibody Fab Heavy Chain


Mass: 23981.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody Fab Lambda Light Chain


Mass: 23257.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 2 types, 3 molecules

#5: 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
#6: 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.: 2
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 , 6 types, 303 molecules

#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 3.31 Å3/Da / Density % sol: 62.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: 10.5% PEG 3K, 100mM NaAco 5.2, 50mM NaCl, Cryoprotectant: 25% glycerol, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 75 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03333 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2008
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03333 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 71438 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 20.7 % / Rsym value: 0.11 / Net I/σ(I): 30.9
Reflection shellResolution: 2.2→2.257 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.32 / Rsym value: 0.79 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0070refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1ADQ, 1RUZ

1adq

1ruz


Resolution: 2.2→39.72 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.108 / SU ML: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24142 3391 5.1 %RANDOM
Rwork0.20487 ---
obs0.20674 62751 95.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.767 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6167 0 131 293 6591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226474
X-RAY DIFFRACTIONr_bond_other_d0.0010.024276
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9648785
X-RAY DIFFRACTIONr_angle_other_deg0.9673.00310401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0355808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24124.816272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87515982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3541523
X-RAY DIFFRACTIONr_chiral_restr0.1010.2977
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217174
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021262
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_it2.01234034
X-RAY DIFFRACTIONr_mcbond_other0.5831658
X-RAY DIFFRACTIONr_mcangle_it3.29556470
X-RAY DIFFRACTIONr_scbond_it5.81482440
X-RAY DIFFRACTIONr_scangle_it7.549112313
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 221 -
Rwork0.433 4528 -
obs--95.32 %
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)
11.615-1.48171.13215.4073-3.43733.6680.07460.2769-0.1199-0.2442-0.02490.02040.14470.2026-0.04970.01110.0014-0.00130.0744-0.02760.0112-64.6657-22.767410.6577
21.0981-0.04320.43760.5711-0.55281.80930.0511-0.0343-0.00830.0244-0.1714-0.40460.23180.59750.12030.17480.0602-0.02010.371-0.00110.3697-22.9579-47.52145.446
32.0019-1.44020.44523.9329-1.00511.8823-0.0699-0.1785-0.10370.5-0.1238-0.34470.26070.56840.19370.29850.0171-0.08580.5290.03060.388-17.9674-54.459361.3031
40.6150.20970.17623.8407-1.8732.2994-0.0095-0.2009-0.23440.4199-0.1186-0.15420.4890.22080.12810.51610.1129-0.06390.54940.02540.4674-24.566-60.052359.697
51.0596-0.40081.08131.3228-0.75653.7833-0.008-0.10130.10290.2688-0.123-0.342-0.10520.49440.1310.0928-0.0105-0.02110.3036-0.03210.2738-26.9465-43.001348.1883
63.8801-3.14492.79173.8196-3.36213.28890.06140.0713-0.1453-0.1224-0.0655-0.07220.14740.22920.0040.01890.01880.00850.0899-0.03390.0493-51.2696-33.491324.4556
70.9610.3701-0.41134.5111-3.25735.4090.08570.14720.1753-0.3339-0.0753-0.0274-0.01430.2568-0.01040.0570.00650.02370.04340.02950.0341-68.848-12.50526.3346
82.3832-3.43872.60018.8038-5.29636.6724-0.1575-0.17030.08640.3860.06010.0262-0.39010.07070.09740.0245-0.0052-0.00250.0315-0.00990.0104-61.5166-15.633225.0451
91.4150.4291-0.40720.1364-0.15770.52980.01120.0540.0805-0.0115-0.01370.00520.01070.17150.00240.17780.0520.00370.14690.0090.1512-45.2967-42.798941.9566
103.4888-5.60415.5489.4427-9.15158.95920.2350.1315-0.1604-0.3466-0.09260.06460.36480.1558-0.14250.03310.0309-0.01480.0498-0.04980.0951-55.0539-45.926137.972
113.9769-4.93173.02059.1517-6.99127.03830.19130.0934-0.2250.00080.14030.7024-0.119-0.3305-0.33160.02760.02540.01990.03660.00090.1381-77.1768-12.173811.7042
127.0628-2.4442-0.06524.1919-0.13655.7229-0.01360.25740.6734-0.2020.04210.0878-0.5783-0.5799-0.02850.17330.08040.05640.08070.0610.1541-80.34223.52674.5365
135.6682.1842-1.36691.3458-1.46192.14370.0004-0.3931-0.2178-0.01-0.1317-0.15560.06640.11460.13130.05460.0078-0.01970.0892-0.02010.1245-37.2462-11.57524.9402
147.70272.19230.94153.25290.1422.6937-0.15310.20430.1152-0.11210.1802-0.152-0.08850.0904-0.02710.0076-0.01160.00710.0202-0.01690.0296-44.5955-5.336918.4909
153.23921.5867-2.67552.1989-1.72473.2851-0.04630.1541-0.3088-0.10430.0107-0.1966-0.0078-0.03710.03560.0267-0.02250.03070.0499-0.05140.1048-38.9183-10.070114.3283
167.91581.60070.17751.49090.43442.0985-0.0438-0.44450.32320.14360.0143-0.2196-0.05040.17840.02960.0625-0.0095-0.02930.0545-0.04180.0969-35.3571-2.972422.9478
175.03114.69214.29085.00173.9263.68220.0525-0.063-0.11260.70660.09080.0237-0.03350.0155-0.14330.71060.07820.00840.6318-0.05950.6051-11.19492.344530.5188
184.9337.06793.330610.22554.71742.3534-0.33150.393-0.1103-0.40090.3934-0.3714-0.24370.5655-0.06190.1999-0.0878-0.08120.89430.070.5866-13.28452.980823.5199
193.03891.06922.11491.01351.28035.6292-0.13880.14610.1849-0.07910.0917-0.0481-0.43220.18820.04710.44490.007-0.05590.18390.00870.3347-45.710318.541219.2691
204.6644-0.6417-0.42426.3515-0.70714.4556-0.1422-0.34610.44180.1523-0.0240.0319-0.1356-0.24580.16620.07310.01120.01260.0506-0.06580.121-48.11477.849724.6744
213.51170.2331.43893.1460.99584.8234-0.1907-0.36920.37890.30490.07630.2309-0.651-0.49550.11440.26220.1088-0.00680.2026-0.08930.2838-52.06715.256328.0563
224.45510.2896-0.06756.38741.22245.7245-0.33720.61240.141-0.85260.02910.2916-0.5629-0.28530.30820.1872-0.0173-0.01380.117-0.0120.2219-47.2536.262713.9467
233.22743.34972.27534.61722.53366.6451-0.3245-0.13050.4168-0.09150.0856-0.1012-1.2770.41670.2390.3625-0.0127-0.1160.1457-0.06890.3629-40.590614.474623.0681
242.125-0.18561.34563.3519-1.07981.1372-0.0361-0.01120.14930.0166-0.02510.2443-0.10840.03650.06120.5109-0.03460.02220.5881-0.07270.5819-12.779615.271427.8105
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 43
2X-RAY DIFFRACTION2A44 - 149
3X-RAY DIFFRACTION3A150 - 190
4X-RAY DIFFRACTION4A191 - 239
5X-RAY DIFFRACTION5A240 - 283
6X-RAY DIFFRACTION6A284 - 326
7X-RAY DIFFRACTION7B1 - 37
8X-RAY DIFFRACTION8B38 - 57
9X-RAY DIFFRACTION9B58 - 73
10X-RAY DIFFRACTION10B74 - 102
11X-RAY DIFFRACTION11B103 - 142
12X-RAY DIFFRACTION12B143 - 173
13X-RAY DIFFRACTION13H1 - 29
14X-RAY DIFFRACTION14H30 - 57
15X-RAY DIFFRACTION15H58 - 84
16X-RAY DIFFRACTION16H85 - 122
17X-RAY DIFFRACTION17H123 - 175
18X-RAY DIFFRACTION18H176 - 188
19X-RAY DIFFRACTION19L3 - 29
20X-RAY DIFFRACTION20L30 - 50
21X-RAY DIFFRACTION21L51 - 83
22X-RAY DIFFRACTION22L84 - 95
23X-RAY DIFFRACTION23L96 - 106
24X-RAY DIFFRACTION24L128 - 195

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