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- PDB-7rdh: Crystal structure of the de novo designed binding protein H3mb in... -

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Basic information

Entry
Database: PDB / ID: 7rdh
TitleCrystal structure of the de novo designed binding protein H3mb in complex with the 1968 influenza A virus hemagglutinin
Components
  • (Hemagglutinin ...) x 2
  • De novo designed protein H3mb
KeywordsVIRAL PROTEIN/DE NOVO PROTEIN / de novo design / mini protein / HA stem binder / VIRAL PROTEIN / VIRAL PROTEIN-DE NOVO PROTEIN 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 Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsKadam, R.U. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI127371 United States
CitationJournal: Nature / Year: 2022
Title: Design of protein-binding proteins from the target structure alone.
Authors: Cao, L. / Coventry, B. / Goreshnik, I. / Huang, B. / Sheffler, W. / Park, J.S. / Jude, K.M. / Markovic, I. / Kadam, R.U. / Verschueren, K.H.G. / Verstraete, K. / Walsh, S.T.R. / Bennett, N. ...Authors: Cao, L. / Coventry, B. / Goreshnik, I. / Huang, B. / Sheffler, W. / Park, J.S. / Jude, K.M. / Markovic, I. / Kadam, R.U. / Verschueren, K.H.G. / Verstraete, K. / Walsh, S.T.R. / Bennett, N. / Phal, A. / Yang, A. / Kozodoy, L. / DeWitt, M. / Picton, L. / Miller, L. / Strauch, E.M. / DeBouver, N.D. / Pires, A. / Bera, A.K. / Halabiya, S. / Hammerson, B. / Yang, W. / Bernard, S. / Stewart, L. / Wilson, I.A. / Ruohola-Baker, H. / Schlessinger, J. / Lee, S. / Savvides, S.N. / Garcia, K.C. / Baker, D.
History
DepositionJul 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.2Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: De novo designed protein H3mb
H: De novo designed protein H3mb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,39420
Polymers206,9928
Non-polymers4,40112
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39500 Å2
ΔGint-120 kcal/mol
Surface area63810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.916, 240.845, 70.704
Angle α, β, γ (deg.)90.000, 117.304, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 9 through 23 or resid 25...
d_2ens_1(chain "C" and (resid 9 through 23 or resid 25...
d_3ens_1(chain "E" and (resid 9 through 23 or resid 25...
d_1ens_2(chain "B" and (resid 1 through 9 or resid 11...
d_2ens_2(chain "D" and (resid 1 through 9 or resid 11...
d_3ens_2(chain "F" and (resid 1 through 9 or resid 11...
d_1ens_3(chain "G" and ((resid 1 through 2 and (name N...
d_2ens_3(chain "H" and (resid 1 through 11 or (resid 12...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROGLYA1 - 15
d_12ens_1LEUASPA17 - 69
d_13ens_1PHESERA71 - 128
d_14ens_1ALALEUA130 - 218
d_15ens_1ARGTYRA221 - 225
d_16ens_1THRLYSA227 - 251
d_17ens_1ARGPROA253 - 265
d_18ens_1ASPPROA267 - 316
d_19ens_1NAGNAGB
d_110ens_1NAGNAGC
d_111ens_1NAGNAGE
d_112ens_1NAGNAGF
d_21ens_1PROGLYJ1 - 15
d_22ens_1LEUASPJ17 - 69
d_23ens_1PHESERJ71 - 128
d_24ens_1ALALEUJ130 - 218
d_25ens_1ARGTYRJ221 - 225
d_26ens_1THRLYSJ227 - 251
d_27ens_1ARGPROJ253 - 265
d_28ens_1ASPPROJ267 - 316
d_29ens_1NAGNAGK
d_210ens_1NAGNAGL
d_211ens_1NAGNAGN
d_212ens_1NAGNAGO
d_31ens_1PROGLYS1 - 15
d_32ens_1LEUASPS17 - 69
d_33ens_1PHESERS71 - 128
d_34ens_1ALALEUS130 - 218
d_35ens_1ARGTYRS221 - 225
d_36ens_1THRLYSS227 - 251
d_37ens_1ARGPROS253 - 265
d_38ens_1ASPPROS267 - 316
d_39ens_1NAGNAGV
d_310ens_1NAGNAGW
d_311ens_1NAGNAGY
d_312ens_1NAGNAGZ
d_11ens_2GLYPHEG1 - 9
d_12ens_2GLUGLYG11 - 16
d_13ens_2ILELYSG18 - 39
d_14ens_2THRGLNG41 - 47
d_15ens_2ASNGLYG49 - 50
d_16ens_2LEUARGG52 - 76
d_17ens_2GLNASPG78 - 164
d_18ens_2ALAPHEG166 - 171
d_21ens_2GLYPHER1 - 9
d_22ens_2GLUGLYR11 - 16
d_23ens_2ILELYSR18 - 39
d_24ens_2THRGLNR41 - 47
d_25ens_2ASNGLYR49 - 50
d_26ens_2LEUARGR52 - 76
d_27ens_2GLNASPR78 - 164
d_28ens_2ALAPHER166 - 171
d_31ens_2GLYPHEAA1 - 9
d_32ens_2GLUGLYAA11 - 16
d_33ens_2ILELYSAA18 - 39
d_34ens_2THRGLNAA41 - 47
d_35ens_2ASNGLYAA49 - 50
d_36ens_2LEUARGAA52 - 76
d_37ens_2GLNASPAA78 - 164
d_38ens_2ALAPHEAA166 - 171
d_11ens_3SERHISG1 - 57
d_21ens_3SERHISH1 - 57

NCS ensembles :
ID
ens_1
ens_2
ens_3

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Components

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Hemagglutinin ... , 2 types, 6 molecules ACEBDF

#1: Protein Hemagglutinin HA1 chain


Mass: 35506.949 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7
#2: Protein Hemagglutinin HA2 chain


Mass: 27230.078 Da / Num. of mol.: 3 / Mutation: R123G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (strain A/Hong Kong/1/1968 H3N2)
Strain: A/Hong Kong/1/1968 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91MA7

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Protein / Non-polymers , 2 types, 96 molecules GH

#3: Protein De novo designed protein H3mb


Mass: 9390.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 3 types, 12 molecules

#4: 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.: 5 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: 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.: 2 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-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.: 5 / Source method: obtained synthetically / 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 ligand of interestN
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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium thiocyanate and 20% (w/v) polyethylene glycol 3350 as a precipitant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.75→60 Å / Num. obs: 47866 / % possible obs: 89.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 57.25 Å2 / CC1/2: 0.79 / Net I/σ(I): 9
Reflection shellResolution: 2.75→2.8 Å / Num. unique obs: 1481 / CC1/2: 0.31

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FNK

4fnk


Resolution: 2.75→43.24 Å / SU ML: 0.5053 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.6
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2889 2359 4.94 %
Rwork0.2323 45366 -
obs0.235 47725 88.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.28 Å2
Refinement stepCycle: LAST / Resolution: 2.75→43.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12296 0 288 94 12678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002113071
X-RAY DIFFRACTIONf_angle_d0.468417762
X-RAY DIFFRACTIONf_chiral_restr0.04272024
X-RAY DIFFRACTIONf_plane_restr0.00372306
X-RAY DIFFRACTIONf_dihedral_angle_d11.22014786
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.697983134152
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS4.7659179042
ens_2d_2GX-RAY DIFFRACTIONTorsion NCS0.511544857503
ens_2d_3GX-RAY DIFFRACTIONTorsion NCS0.585600834209
ens_3d_2HX-RAY DIFFRACTIONTorsion NCS0.779962105845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.810.4061770.34071644X-RAY DIFFRACTION53.66
2.81-2.870.4027830.35271659X-RAY DIFFRACTION56.65
2.87-2.940.38441090.33482116X-RAY DIFFRACTION69.23
2.94-3.010.41081610.33832513X-RAY DIFFRACTION86.57
3.01-3.090.40711640.29812681X-RAY DIFFRACTION89.44
3.09-3.180.3481960.2792782X-RAY DIFFRACTION93.62
3.18-3.280.34341630.27652791X-RAY DIFFRACTION95.6
3.28-3.40.31571280.26482957X-RAY DIFFRACTION97.63
3.4-3.540.3691190.2612987X-RAY DIFFRACTION97.86
3.54-3.70.30781260.24452926X-RAY DIFFRACTION96.86
3.7-3.890.29421450.23432904X-RAY DIFFRACTION96.92
3.89-4.140.27861490.22622837X-RAY DIFFRACTION94.91
4.14-4.460.2611510.19942792X-RAY DIFFRACTION93.55
4.46-4.90.25571320.19422950X-RAY DIFFRACTION97.59
4.9-5.610.25941950.19672917X-RAY DIFFRACTION98.51
5.61-7.060.24121260.21492999X-RAY DIFFRACTION98.39
7.07-43.240.20611350.19622911X-RAY DIFFRACTION95.64

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