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Open data
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Basic information
Entry | Database: PDB / ID: 5w1k | |||||||||||||||||||||
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Title | JUNV GP1 CR1-10 Fab CR1-28 Fab complex | |||||||||||||||||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / Fab / antibody / Junin virus / arenavirus / viral protein / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||||||||||||||
Function / homology | ![]() immunoglobulin complex / host cell Golgi membrane / immunoglobulin mediated immune response / antigen binding / adaptive immune response / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / blood microparticle / immune response / fusion of virus membrane with host endosome membrane ...immunoglobulin complex / host cell Golgi membrane / immunoglobulin mediated immune response / antigen binding / adaptive immune response / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / blood microparticle / immune response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular space / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Raymond, D.D. / Clark, L.E. / Abraham, J. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Vaccine-elicited receptor-binding site antibodies neutralize two New World hemorrhagic fever arenaviruses. Authors: Clark, L.E. / Mahmutovic, S. / Raymond, D.D. / Dilanyan, T. / Koma, T. / Manning, J.T. / Shankar, S. / Levis, S.C. / Briggiler, A.M. / Enria, D.A. / Wucherpfennig, K.W. / Paessler, S. / Abraham, J. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 772.9 KB | Display | ![]() |
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PDB format | ![]() | 629.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 81.8 KB | Display | |
Data in CIF | ![]() | 125.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w1gC ![]() 5w1mC ![]() 5en2S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules EJPR
#5: Protein | Mass: 16425.861 Da / Num. of mol.: 4 / Fragment: UNP residues 87-228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Antibody , 4 types, 16 molecules AFKSBGLTCHMNDIOQ
#1: Antibody | Mass: 22621.170 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 24168.881 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Antibody | Mass: 23149.621 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Antibody | Mass: 23785.506 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 3 types, 5 molecules ![](data/chem/img/NAG.gif)
#6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-NAG / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.89 Å3/Da / Density % sol: 68.35 % |
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Crystal grow | Temperature: 297 K / Method: batch mode / pH: 7.7 / Details: 1.9 M AmSO4 pH 7.7 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.99→49.35 Å / Num. obs: 57195 / % possible obs: 99.1 % / Redundancy: 3.401 % / Biso Wilson estimate: 22.23 Å2 / CC1/2: 0.796 / Rmerge(I) obs: 0.721 / Rrim(I) all: 0.857 / Χ2: 0.801 / Net I/σ(I): 2.34 / Num. measured all: 194531 / Scaling rejects: 78 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5EN2 Resolution: 3.99→49.35 Å / Cor.coef. Fo:Fc: 0.81 / Cor.coef. Fo:Fc free: 0.725 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.812
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Displacement parameters | Biso max: 173 Å2 / Biso mean: 69 Å2 / Biso min: 22.14 Å2
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Refine analyze | Luzzati coordinate error obs: 0.78 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.99→49.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.99→4.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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