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- PDB-6cfe: Crystal structure of C2S5: A computationally designed immunogen t... -

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Basic information

Entry
Database: PDB / ID: 6cfe
TitleCrystal structure of C2S5: A computationally designed immunogen to target Carbohydrate-Occluded Epitopes on the HIV envelope
ComponentsMutant of Apolipoprotein E3 (APO-E3)
KeywordsLIPID TRANSPORT / Immunogen / HIV-1 / gp120 / Protein Design / Mutant of APOLIPOPROTEIN E3 (APO-E3)
Function / homologyApolipoprotein / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.994 Å
AuthorsZhu, C. / Ke, H.M. / Swanstrom, R. / Dokholyan, N.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI102732 United States
CitationJournal: Nat Commun / Year: 2019
Title: Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies.
Authors: Zhu, C. / Dukhovlinova, E. / Council, O. / Ping, L. / Faison, E.M. / Prabhu, S.S. / Potter, E.L. / Upton, S.L. / Yin, G. / Fay, J.M. / Kincer, L.P. / Spielvogel, E. / Campbell, S.L. / ...Authors: Zhu, C. / Dukhovlinova, E. / Council, O. / Ping, L. / Faison, E.M. / Prabhu, S.S. / Potter, E.L. / Upton, S.L. / Yin, G. / Fay, J.M. / Kincer, L.P. / Spielvogel, E. / Campbell, S.L. / Benhabbour, S.R. / Ke, H. / Swanstrom, R. / Dokholyan, N.V.
History
DepositionFeb 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Mutant of Apolipoprotein E3 (APO-E3)


Theoretical massNumber of molelcules
Total (without water)18,6431
Polymers18,6431
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.883, 46.883, 140.417
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Mutant of Apolipoprotein E3 (APO-E3)


Mass: 18643.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET14b / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 16% PEG 20000, 100 mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 12904 / % possible obs: 99.8 % / Redundancy: 18 % / Biso Wilson estimate: 42.97 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.015 / Rrim(I) all: 0.066 / Χ2: 1.678 / Net I/σ(I): 13.6 / Num. measured all: 232314
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0316.50.8866560.8880.2090.9120.87298.1
2.03-2.0717.70.7856080.90.1820.8060.872100
2.07-2.1117.30.5756210.9490.1330.5910.896100
2.11-2.1517.20.4856330.9560.1130.4990.90699.5
2.15-2.217.40.386170.9760.0890.3910.976100
2.2-2.2517.20.3116380.9810.0730.320.996100
2.25-2.3117.50.2716100.9890.0640.2791.039100
2.31-2.3717.70.2276560.9910.0530.2331.1299.8
2.37-2.4417.60.1766320.9940.0410.1811.20199.8
2.44-2.5217.80.1386230.9960.0330.1421.319100
2.52-2.6117.70.1266690.9980.030.131.31599.9
2.61-2.7117.60.1076160.9970.0250.111.46100
2.71-2.8418.30.0916220.9980.0210.0941.589100
2.84-2.9918.20.086440.9980.0190.0831.70999.8
2.99-3.1718.20.0696620.9990.0160.0712.052100
3.17-3.4218.60.0666430.9990.0150.0682.574100
3.42-3.7619.10.0636680.9990.0150.0643.174100
3.76-4.3119.20.0616620.9990.0140.0633.665100
4.31-5.4320.20.0486740.9990.0110.0492.57399.9
5.43-5018.40.0447500.9990.0110.0452.18199.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BZ4

1bz4


Resolution: 1.994→39.004 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2687 637 4.96 %
Rwork0.2365 12212 -
obs0.2381 12849 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.73 Å2 / Biso mean: 70.1714 Å2 / Biso min: 27.96 Å2
Refinement stepCycle: final / Resolution: 1.994→39.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 0 17 1175
Biso mean---48.78 -
Num. residues----141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041170
X-RAY DIFFRACTIONf_angle_d0.5131572
X-RAY DIFFRACTIONf_chiral_restr0.028175
X-RAY DIFFRACTIONf_plane_restr0.002205
X-RAY DIFFRACTIONf_dihedral_angle_d13.967731
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.994-2.1480.37091210.29422384250599
2.148-2.36410.32571240.267123932517100
2.3641-2.70610.29921260.275224122538100
2.7061-3.40910.35251270.276224402567100
3.4091-39.01150.21271390.201325832722100
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)
13.27520.24950.37832.57581.70063.1995-0.07790.5157-0.1674-0.39630.1567-0.1444-0.487-0.03830.00010.41140.02490.05890.396-0.01820.36118.947-12.439-10.428
21.72490.1042-0.21670.0937-0.25180.9656-0.18540.18720.6038-0.0472-0.12980.5705-0.1156-0.5991-0.00040.59130.1397-0.01430.6865-0.0820.5327-4.263-9.678-9.634
31.959-0.3639-0.50990.60880.93182.730.4067-0.21240.48860.3375-0.56390.41540.3767-0.78130.00320.36330.0550.05720.5302-0.00510.45974.487-9.7420.855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 23:80 )A23 - 80
2X-RAY DIFFRACTION2( CHAIN A AND RESID 81:123 )A81 - 123
3X-RAY DIFFRACTION3( CHAIN A AND RESID 124:159 )A124 - 159

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