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Yorodumi- PDB-4jan: crystal structure of broadly neutralizing antibody CH103 in compl... -
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-Basic information
Entry | Database: PDB / ID: 4jan | ||||||
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Title | crystal structure of broadly neutralizing antibody CH103 in complex with HIV-1 gp120 | ||||||
Components |
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Keywords | viral protein/immune system / HIV-1 / gp120 / GLYCOPROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM COMPLEX / Antibody / immunoglobulin / NEUTRALIZATION / VACCINE | ||||||
Function / homology | Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / viral envelope / Immunoglobulin-like / Sandwich / Mainly Beta / ENVELOPE GLYCOPROTEIN GP120 of HIV-1 clade C Function and homology information | ||||||
Biological species | HUMAN IMMUNODEFICIENCY VIRUS 1 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | ||||||
Authors | Zhou, T. / Moquin, S. / Zheng, A. / Srivatsan, S. / Kwong, P.D. | ||||||
Citation | Journal: Nature / Year: 2013 Title: Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Authors: Liao, H.X. / Lynch, R. / Zhou, T. / Gao, F. / Alam, S.M. / Boyd, S.D. / Fire, A.Z. / Roskin, K.M. / Schramm, C.A. / Zhang, Z. / Zhu, J. / Shapiro, L. / Mullikin, J.C. / Gnanakaran, S. / ...Authors: Liao, H.X. / Lynch, R. / Zhou, T. / Gao, F. / Alam, S.M. / Boyd, S.D. / Fire, A.Z. / Roskin, K.M. / Schramm, C.A. / Zhang, Z. / Zhu, J. / Shapiro, L. / Mullikin, J.C. / Gnanakaran, S. / Hraber, P. / Wiehe, K. / Kelsoe, G. / Yang, G. / Xia, S.M. / Montefiori, D.C. / Parks, R. / Lloyd, K.E. / Scearce, R.M. / Soderberg, K.A. / Cohen, M. / Kamanga, G. / Louder, M.K. / Tran, L.M. / Chen, Y. / Cai, F. / Chen, S. / Moquin, S. / Du, X. / Joyce, M.G. / Srivatsan, S. / Zhang, B. / Zheng, A. / Shaw, G.M. / Hahn, B.H. / Kepler, T.B. / Korber, B.T. / Kwong, P.D. / Mascola, J.R. / Haynes, B.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jan.cif.gz | 661.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jan.ent.gz | 559.2 KB | Display | PDB format |
PDBx/mmJSON format | 4jan.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jan_validation.pdf.gz | 507.6 KB | Display | wwPDB validaton report |
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Full document | 4jan_full_validation.pdf.gz | 518.7 KB | Display | |
Data in XML | 4jan_validation.xml.gz | 41.6 KB | Display | |
Data in CIF | 4jan_validation.cif.gz | 55.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/4jan ftp://data.pdbj.org/pub/pdb/validation_reports/ja/4jan | HTTPS FTP |
-Related structure data
Related structure data | 4jamC 3ngbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Antibody , 2 types, 4 molecules HALB
#2: Antibody | Mass: 23896.832 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: CMVR-based / Cell line (production host): 293F / Production host: HOMO SAPIENS (human) #3: Antibody | Mass: 22533.926 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: CMVR-based / Cell line (production host): 293F / Production host: HOMO SAPIENS (human) |
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-Protein / Sugars , 2 types, 12 molecules GI
#1: Protein | Mass: 39273.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Strain: ZM176.55 / Plasmid: CMVR-based / Cell line (production host): 293F / Production host: HOMO SAPIENS (human) / References: UniProt: R4GRV3*PLUS #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 3 types, 26 molecules
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.73 % |
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: 200 mM sodium formate, 20% PEG 3350 and 100 mM Bistrispropane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MAR CCD 300MM / Detector: CCD / Date: Jul 22, 2012 / Details: APS 22ID |
Radiation | Monochromator: APS 22ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→50 Å / Num. obs: 20488 / % possible obs: 89.4 % / Observed criterion σ(I): 1.4 / Redundancy: 3.4 % / Biso Wilson estimate: 61.3 Å2 / Rsym value: 0.134 / Net I/σ(I): 10 |
Reflection shell | Resolution: 3.21→3.25 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.31 / % possible all: 59 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NGB Resolution: 3.15→46.75 Å / SU ML: 0.4 / σ(F): 1.37 / Phase error: 28.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.15→46.75 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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