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- PDB-4eef: Crystal structure of the designed inhibitor protein F-HB80.4 in c... -

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Basic information

Entry
Database: PDB / ID: 4eef
TitleCrystal structure of the designed inhibitor protein F-HB80.4 in complex with the 1918 influenza virus hemagglutinin.
Components
  • F-HB80.4, DESIGNED HEMAGGLUTININ BINDING PROTEIN
  • Hemagglutinin HA1 chain
  • Hemagglutinin HA2 chain
KeywordsIMMUNE SYSTEM/INHIBITOR / immunoglobulin / hemagglutinin / Fusion of virus membrane with host membrane / membrane fusion / Sialic acid / Virion / IMMUNE SYSTEM / IMMUNE SYSTEM-INHIBITOR 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 / Homeodomain-like / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin ...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 / Homeodomain-like / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Artificial Gene (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.704 Å
AuthorsDreyfus, C. / Wilson, I.A.
CitationJournal: Nat.Biotechnol. / Year: 2012
Title: Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing.
Authors: Whitehead, T.A. / Chevalier, A. / Song, Y. / Dreyfus, C. / Fleishman, S.J. / De Mattos, C. / Myers, C.A. / Kamisetty, H. / Blair, P. / Wilson, I.A. / Baker, D.
History
DepositionMar 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: 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 / 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_unobs_or_zero_occ_atoms / 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.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: F-HB80.4, DESIGNED HEMAGGLUTININ BINDING PROTEIN
H: F-HB80.4, DESIGNED HEMAGGLUTININ BINDING PROTEIN
I: F-HB80.4, DESIGNED HEMAGGLUTININ BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,73412
Polymers196,9749
Non-polymers1,7603
Water2,504139
1
A: Hemagglutinin HA1 chain
B: Hemagglutinin HA2 chain
G: F-HB80.4, DESIGNED HEMAGGLUTININ BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2454
Polymers65,6583
Non-polymers5871
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-38 kcal/mol
Surface area27090 Å2
MethodPISA
2
C: Hemagglutinin HA1 chain
D: Hemagglutinin HA2 chain
H: F-HB80.4, DESIGNED HEMAGGLUTININ BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2454
Polymers65,6583
Non-polymers5871
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-41 kcal/mol
Surface area26690 Å2
MethodPISA
3
E: Hemagglutinin HA1 chain
F: Hemagglutinin HA2 chain
I: F-HB80.4, DESIGNED HEMAGGLUTININ BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2454
Polymers65,6583
Non-polymers5871
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-35 kcal/mol
Surface area26800 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35760 Å2
ΔGint-159 kcal/mol
Surface area67450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.333, 126.151, 243.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hemagglutinin HA1 chain / Hemagglutinin HA1 chain


Mass: 36452.797 Da / Num. of mol.: 3
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): HIGH FIVE / References: UniProt: Q9WFX3
#2: Protein Hemagglutinin HA2 chain / Hemagglutinin HA2 chain


Mass: 20394.445 Da / Num. of mol.: 3
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): HIGH FIVE / References: UniProt: Q9WFX3
#3: Protein F-HB80.4, DESIGNED HEMAGGLUTININ BINDING PROTEIN


Mass: 8810.759 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Artificial Gene (others) / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2 (BL21/DE3)
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 16% PEG3350, and 100mM Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03326 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2011
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03326 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 58197 / Num. obs: 58197 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
XPREPdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.704→43.673 Å / SU ML: 0.85 / σ(F): 1.34 / Phase error: 29.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.285 2939 5.06 %Random
Rwork0.2286 ---
all0.2314 58120 --
obs0.2314 58120 94.06 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.165 Å2 / ksol: 0.294 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--12.7078 Å2-0 Å20 Å2
2---1.6512 Å2-0 Å2
3---14.359 Å2
Refinement stepCycle: LAST / Resolution: 2.704→43.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12589 0 117 139 12845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913063
X-RAY DIFFRACTIONf_angle_d1.34417731
X-RAY DIFFRACTIONf_dihedral_angle_d20.8774696
X-RAY DIFFRACTIONf_chiral_restr0.0931938
X-RAY DIFFRACTIONf_plane_restr0.0072299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.704-2.74860.41921090.31332184X-RAY DIFFRACTION79
2.7486-2.7960.33421310.29412435X-RAY DIFFRACTION88
2.796-2.84680.34891460.28852535X-RAY DIFFRACTION94
2.8468-2.90150.34331410.27492581X-RAY DIFFRACTION93
2.9015-2.96080.32631570.26952529X-RAY DIFFRACTION93
2.9608-3.02510.39081380.2712565X-RAY DIFFRACTION92
3.0251-3.09550.31331240.26112554X-RAY DIFFRACTION92
3.0955-3.17290.34921270.25552565X-RAY DIFFRACTION93
3.1729-3.25860.3381350.25662578X-RAY DIFFRACTION93
3.2586-3.35450.34371520.24272541X-RAY DIFFRACTION93
3.3545-3.46270.33031150.25112588X-RAY DIFFRACTION92
3.4627-3.58640.29811510.23082555X-RAY DIFFRACTION93
3.5864-3.72990.27031530.23212576X-RAY DIFFRACTION93
3.7299-3.89960.28951520.22422615X-RAY DIFFRACTION95
3.8996-4.1050.26221540.20442724X-RAY DIFFRACTION97
4.105-4.3620.2651310.19452806X-RAY DIFFRACTION99
4.362-4.69840.21911430.18242805X-RAY DIFFRACTION100
4.6984-5.17060.25771390.1942854X-RAY DIFFRACTION100
5.1706-5.91720.27371350.22582836X-RAY DIFFRACTION100
5.9172-7.44910.27351530.23842886X-RAY DIFFRACTION100
7.4491-43.67910.261530.23542869X-RAY DIFFRACTION95

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