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- PDB-1ggi: CRYSTAL STRUCTURE OF AN HIV-1 NEUTRALIZING ANTIBODY 50.1 IN COMPL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ggi | ||||||
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Title | CRYSTAL STRUCTURE OF AN HIV-1 NEUTRALIZING ANTIBODY 50.1 IN COMPLEX WITH ITS V3 LOOP PEPTIDE ANTIGEN | ||||||
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![]() | IMMUNOGLOBULIN | ||||||
Function / homology | ![]() Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of establishment of T cell polarity / host cell endosome membrane / complement activation, classical pathway / antigen binding / antibacterial humoral response ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of establishment of T cell polarity / host cell endosome membrane / complement activation, classical pathway / antigen binding / antibacterial humoral response / clathrin-dependent endocytosis of virus by host cell / viral protein processing / blood microparticle / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / extracellular exosome / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Stanfield, R.L. / Rini, J.M. / Wilson, I.A. | ||||||
![]() | ![]() Title: Crystal structure of a human immunodeficiency virus type 1 neutralizing antibody, 50.1, in complex with its V3 loop peptide antigen. Authors: Rini, J.M. / Stanfield, R.L. / Stura, E.A. / Salinas, P.A. / Profy, A.T. / Wilson, I.A. #1: ![]() Title: Crystallization, Sequence, and Preliminary Crystallographic Data for an Antipeptide Fab 50.1 And Peptide Complexes with the Principal Neutralizing Determinant of HIV-1 Gp120 Authors: Stura, E.A. / Stanfield, R.L. / Fieser, G.G. / Silver, S. / Rogusca, M. / Hincapie, L.M. / Simmerman, H.K.B. / Profy, A.T. / Wilson, I.A. #2: ![]() Title: Major Antigen-Induced Domain Rearrangements in an Antibody Authors: Stanfield, R.L. / Takimoto-Kamimura, M. / Rini, J.M. / Profy, A.T. / Wilson, I.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162.5 KB | Display | ![]() |
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PDB format | ![]() | 128.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 409.8 KB | Display | ![]() |
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Full document | ![]() | 450.6 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 33 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Unit cell |
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Atom site foot note | 1: RESIDUES 8, 77, 95, 141, 204 OF THE L AND M CHAINS, AND RESIDUES 149, 151, 200 OF THE H AND J CHAINS ARE CIS PROLINES. | ||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THERE ARE TWO FAB MOLECULES IN THE ASYMMETRIC UNIT. THE TRANSFORMATIONS GIVEN ON *MTRIX* RECORDS BELOW YIELD APPROXIMATE COORDINATES FOR CHAINS *L* AND *H* WHEN APPLIED TO CHAINS *M* AND *J*. THESE TRANSFORMATIONS HAVE BEEN PROVIDED SEPARATELY FOR THE VH AND CH DOMAINS OF THE HEAVY CHAIN AND THE VL AND CL DOMAINS OF THE LIGHT CHAIN. THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR THE VL DOMAIN OF CHAIN *L* WHEN APPLIED TO THE VL DOMAIN OF CHAIN *M*. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR THE CL DOMAIN OF CHAIN *L* WHEN APPLIED TO THE CL DOMAIN OF CHAIN *M*. THE TRANSFORMATION PRESENTED ON *MTRIX 3* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR THE VH DOMAIN OF CHAIN *H* WHEN APPLIED TO THE VH DOMAIN OF CHAIN *J*. THE TRANSFORMATION PRESENTED ON *MTRIX 4* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR THE CH DOMAIN OF CHAIN *H* WHEN APPLIED TO THE CH DOMAIN OF CHAIN *J*. |
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Components
#1: Antibody | Mass: 23994.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 23828.807 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source References: UniProt: P01863 #3: Protein/peptide | Mass: 1827.182 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source References: UniProt: P05877*PLUS Sequence details | THE FAB FRAGMENT IS NUMBERED BY THE CONVENTION OF E. KABAT (E.A. KABAT, T.T. WU, M. REID-MILLER, H. ...THE FAB FRAGMENT IS NUMBERED BY THE CONVENTION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.14 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.5 / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.8 Å / % possible obs: 81 % / Rmerge(I) obs: 0.1 |
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Processing
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Refinement | Rfactor Rwork: 0.188 / Rfactor obs: 0.188 / Highest resolution: 2.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 10 Å / Rfactor obs: 0.188 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.79 |