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Open data
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Basic information
Entry | Database: PDB / ID: 7lyw | ||||||
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Title | Crystal structure of the HCMV pentamer-specific antibody 2-25 | ||||||
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![]() | IMMUNE SYSTEM / antibody / Fab / HCMV pentamer / cytomegalovirus | ||||||
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Method | ![]() ![]() ![]() | ||||||
![]() | Wrapp, D. / Mishra, A.K. / McLellan, J.S. | ||||||
![]() | ![]() Title: Structural basis for HCMV Pentamer recognition by neuropilin 2 and neutralizing antibodies. Authors: Daniel Wrapp / Xiaohua Ye / Zhiqiang Ku / Hang Su / Harrison G Jones / Nianshuang Wang / Akaash K Mishra / Daniel C Freed / Fengsheng Li / Aimin Tang / Leike Li / Dabbu Kumar Jaijyan / Hua ...Authors: Daniel Wrapp / Xiaohua Ye / Zhiqiang Ku / Hang Su / Harrison G Jones / Nianshuang Wang / Akaash K Mishra / Daniel C Freed / Fengsheng Li / Aimin Tang / Leike Li / Dabbu Kumar Jaijyan / Hua Zhu / Dai Wang / Tong-Ming Fu / Ningyan Zhang / Zhiqiang An / Jason S McLellan / ![]() Abstract: Human cytomegalovirus (HCMV) encodes multiple surface glycoprotein complexes to infect a variety of cell types. The HCMV Pentamer, composed of gH, gL, UL128, UL130, and UL131A, enhances entry into ...Human cytomegalovirus (HCMV) encodes multiple surface glycoprotein complexes to infect a variety of cell types. The HCMV Pentamer, composed of gH, gL, UL128, UL130, and UL131A, enhances entry into epithelial, endothelial, and myeloid cells by interacting with the cell surface receptor neuropilin 2 (NRP2). Despite the critical nature of this interaction, the molecular determinants that govern NRP2 recognition remain unclear. Here, we describe the cryo-EM structure of NRP2 bound to Pentamer. The high-affinity interaction between these proteins is calcium dependent and differs from the canonical carboxyl-terminal arginine (CendR) binding that NRP2 typically uses. We also determine the structures of four neutralizing human antibodies bound to the HCMV Pentamer to define susceptible epitopes. Two of these antibodies compete with NRP2 binding, but the two most potent antibodies recognize a previously unidentified epitope that does not overlap the NRP2-binding site. Collectively, these findings provide a structural basis for HCMV tropism and antibody-mediated neutralization. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 260.2 KB | Display | ![]() |
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PDB format | ![]() | 208.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 470.9 KB | Display | ![]() |
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Full document | ![]() | 483.4 KB | Display | |
Data in XML | ![]() | 50.1 KB | Display | |
Data in CIF | ![]() | 71.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7kbaC ![]() 7kbbC ![]() 7lyvC ![]() 7m1cC ![]() 7m22C ![]() 7m30C ![]() 5n4jS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 25189.230 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 22723.951 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.95 Å3/Da / Density % sol: 68.86 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 30% PEG 4000, 0.1M BIS-TRIS pH 6.5, 0.1 M calcium chloride, 0.1 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.51→69.89 Å / Num. obs: 77232 / % possible obs: 98.38 % / Redundancy: 6.8 % / CC1/2: 0.991 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.51→2.57 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 7688 / CC1/2: 0.522 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5N4J Resolution: 2.51→58.08 Å / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Stereochemistry target values: ML
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Solvent computation | Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.79 Å2 / Biso min: 15.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.51→58.08 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27
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