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Open data
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Basic information
Entry | Database: PDB / ID: 5w1m | ||||||||||||||||||
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Title | MACV GP1 CR1-07 Fab complex | ||||||||||||||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / Fab / antibody / Machupo virus / arenavirus / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||||||||||||||
Function / homology | ![]() host cell Golgi membrane / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / blood microparticle / immune response ...host cell Golgi membrane / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral 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 / extracellular exosome / 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 | ![]() | 451.1 KB | Display | ![]() |
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PDB format | ![]() | 370.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 81.7 KB | Display | |
Data in CIF | ![]() | 110.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w1gC ![]() 5w1kC ![]() 2wfoS 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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1 | ![]()
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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 QRST
#3: Protein | Mass: 17454.875 Da / Num. of mol.: 4 / Fragment: UNP residues 87-238 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Antibody , 2 types, 8 molecules ACEGBDFH
#1: Antibody | Mass: 24289.822 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 24291.330 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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-Sugars , 4 types, 5 molecules ![](data/chem/img/BMA.gif)
![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #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 | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-BMA / | #7: Sugar | ChemComp-NAG / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.87 Å3/Da / Density % sol: 74.74 % |
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Crystal grow | Temperature: 297 K / Method: batch mode / pH: 5.5 / Details: 1.8 M AmSO4 and 100 mM NaCitrate pH 5.5. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.91→49.12 Å / Num. obs: 46832 / % possible obs: 98.8 % / Redundancy: 8.073 % / Biso Wilson estimate: 145.49 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.329 / Rrim(I) all: 0.351 / Χ2: 1.02 / Net I/σ(I): 7.72 / Num. measured all: 378092 / Scaling rejects: 193 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WFO Resolution: 3.91→49.12 Å / Cor.coef. Fo:Fc: 0.424 / Cor.coef. Fo:Fc free: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.636
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Displacement parameters | Biso max: 108.13 Å2 / Biso mean: 33.45 Å2 / Biso min: 11.07 Å2
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Refine analyze | Luzzati coordinate error obs: 0.81 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.91→49.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.91→4.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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