Primary Citation PubMed: 9048542
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Identifying foldable regions in protein sequence from the hydrophobic signal.
(2008) Nucleic Acids Res 36
PubMed: 18056079 | PubMedCentral: PMC2241846 | DOI: 10.1093/nar/gkm1070
( b ) IgG2 monoclonal antibody heavy chain from Mus musculus (PDB 1IGT, chain B), coloured according to the linker prediction by Scooby–Domain.
Figure 7 b demonstrates how Scooby-Domain accurately delineated the monoclonal antibody heavy chain for Mus musculus (PDB 1IGT, chain B).
Publication Year: 2008
Illuminating the life of GPCRs.
(2009) Cell Commun Signal 7
PubMed: 19602276 | PubMedCentral: PMC2726148 | DOI: 10.1186/1478-811X-7-16
Representation of a GPCR based on the structure of sensory rhodopsin II (A; Protein Data Bank identifier (PDB ID), 1GUE ), the structure of the peptide ligand porcine neuropeptide Y (B; PDB ID, 1F8P )... the structure of an auto-fluorescent protein, namely the S65A/Y66F GFP variant (C; PDB ID, 2HGD ), the structure of an immunoglobulin gamma (D; PDB ID 1IGT ), the Lumio™-tag (E), the SNAP™-tag based on the structure of the human O 6 -alkylguanine-DNA alkyltransferase, (F; PDB ID, 1EH6 ).
Publication Year: 2009
Immunoglobulin superfamily virus receptors and the evolution of adaptive immunity.
(2009) PLoS Pathog 5
PubMed: 19956667 | PubMedCentral: PMC2777377 | DOI: 10.1371/journal.ppat.1000481
(F) Structural alignment of mFab 231 V L (  ; 1IGT), CD4 D1 (  ; 1CDJ), hJAM-A D1 (  ; 1NBQ), and CAR D1 (  ; 1EAJ) perf... rmed using MODELLER (program Web site: http://salilab.org/modeller/ ).
(A) Ribbon drawing of mFab 231 (left) (  ; 1IGT) and the extracellular domains of hJAM-A (right) (  ; 1NBQ).
IPET and FETR: experimental approach for studying molecular structure dynamics by cryo-electron tomography of a single-molecule structure.
(2012) PLoS One 7
PubMed: 22291925 | PubMedCentral: PMC3265479 | DOI: 10.1371/journal.pone.0030249
Figure S11 The crystal structure of IgG antibody (PDB entry 1IGT) displays a hole within each domain.
(C) Their corresponding orientations of the crystal structure (PDB entry 1IGT) displayed in their corresponding holes within the corresponding domains can also be visualized, suggesting the holes are the intrinsic structure features instead of the artifact from neither negative-staining nor defocus-related contrast transfer function (CTF).
(C) Docking the crystal structure (PDB entry 1IGT) of each domain of the IgG antibody into each ring-shaped density of IgG showed a good fit.
Displaying the crystal structure of the IgG antibody (PDB entry 1IGT) by two methods—the ribbon and Van der Waals surface—both views show holes in the F ab domain ( Figure S11 , the top two domains) and the F c domain ( Figure S11 , the bottom domain).
Publication Year: 2012
Isolation of monoclonal antibodies with predetermined conformational epitope specificity.
PubMed: 22737224 | PubMedCentral: PMC3380854 | DOI: 10.1371/journal.pone.0038943
Molecular graphics image for antibody  (pdb code 1IGT) was produced using the UCSF Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of Californi... , San Francisco (supported by NIH P41 RR001081).
Crystal structure of the conserved domain of the DC lysosomal associated membrane protein: implications for the lysosomal glycocalyx.
(2012) BMC Biol 10
PubMed: 22809326 | PubMedCentral: PMC3409847 | DOI: 10.1186/1741-7007-10-62
Hydrogen bonds connect loop L1 to an adjacent hairpin in chain A, but not in chain B. ( C ) A V H immunoglobulin domain is shown for comparison (PDB 1IGT ).
Function and 3D structure of the N-glycans on glycoproteins.
(2012) Int J Mol Sci 13
PubMed: 22942711 | PubMedCentral: PMC3430242 | DOI: 10.3390/ijms13078398
Figure 2 ( a ) Overall structure of immunoglobulin G (PDB code; 1igt) is shown in a ribbon model.
Natural and man-made V-gene repertoires for antibody discovery.
(2012) Front Immunol 3
PubMed: 23162556 | PubMedCentral: PMC3498902 | DOI: 10.3389/fimmu.2012.00342
Figure 1 Ribbon representation of an intact IgG molecule (PDBID: 1IGT).
Peptide-conjugation induced conformational changes in human IgG1 observed by optimized negative-staining and individual-particle electron tomography.
(2013) Sci Rep 3
PubMed: 23346347 | PubMedCentral: PMC3549606 | DOI: 10.1038/srep01089
(I) Fitting the crystal structure (PDB entry 1IGT) of each domain into these rod-shaped densities of IgG matched poorly.
At specific viewing orientations, manual masks were applied on the raw particle images ( Fig. 1C ) near the particle boundary to reduce outside noise ( Fig. 1D ), revealing that the particle outer features are remarkably similar to crystal structure of an IgG2a antibody (PDB entry 1IGT) 18 , an anti-canine lymphoma monoclonal antibody (mab231) ( Fig. 1E ).
These structural features are consistent to the crystal structure of the IgG antibody (PDB entry 1IGT) 19 , in which the holes of two F ab domains are much smaller than that of the F c domain.
Inserting domain crystal structures (PDB: 1IGT) into its corresponding domain EM density map by Chimera shows a poor match in domain shape, suggesting a conformational change of each domain structure after peptide conjugation ( Fig. 4I and 4L ) .
The three domains of the crystal structure (PDB entry 1IGT 18 ) were fitted into the final IPET 3D density map by using a rigid-body fitting option in UCSF Chimera 20 .
(E) These latter images were compared with the crystal structure of IgG antibody (PDB entry 1IGT) at similar orientations.
(C) Fitting each domain of the crystal structure (PDB entry 1IGT) into each ring-shaped density of IgG respectively matched well 17 .
Publication Year: 2013
Protein molecular surface mapped at different geometrical resolutions.
(2013) PLoS One 8
PubMed: 23516572 | PubMedCentral: PMC3597524 | DOI: 10.1371/journal.pone.0058896
Protein name PDB code Atoms Residues Chains 1 1 α lactalbumin 1A4V 1092 123 1 2 2 porcine β-lactoglobulin 1EXS 1248 160 1 3 bovine β-lactoglobulin 1BEB 2473 324 2 3, Subset 3.1... RMSD(129) = 0.6481 4 hen egg-white lysozyme 1LYZ 1001 129 1 5 turkey egg-white lysozyme 135L 994 129 1 6 hen egg-white lysozyme 2LYM 1001 129 1 7 triciclic lysozyme 2LZT 1001 129 1 3, Subset 3.2 RMSD(164) = 0.24 8 mutant of phage T4 lysozyme 1L35 1305 164 1 9 T4 lysozyme 1LYD 1309 164 1 4 RMSD(124) = 0.1655 10 ribonuclease-A 8RAT 951 124 1 11 ribonuclease-A 1RBX 956 124 1 12 bovine ribonuclease-A 3RN3 957 124 1 13 ribonuclease-A 1AFU 1894 248 2 5, Subset 5.1 RMSD(287) = 0.8877 14 human oxyhemoglobin 1HHO 2192 287 2 15 human carbonmonoxy hemoglobin 2HCO 2192 287 2 16 horse deoxyhemoglobin 2DHB 2201 287 2 5, Subset 5.2 RMSD(574) = 1.501 17 human hemoglobin A 1BUW 4342 574 4 18 human hemoglobin (W37A) 1Y4F 4368 574 4 19 hemoglobin mutant (W37A) 1A01 4368 574 4 20 human hemoglobin (W37E) 1Y4P 4376 574 4 21 hemoglobin mutant (W37Y) 1A00 4382 574 4 22 human hemoglobin (W37Y) 1Y46 4382 574 4 23 human deoxyhemoglobin 2HHB 4384 574 4 24 human hemoglobin (W37G) 1Y4G 4366 574 4 25 hemoglobin mutant (V1M) 1A0U 4386 574 4 26 hemoglobin mutant (V1M) 1A0Z 4386 574 4 27 recombinant hemoglobin 1C7D 4396 576 3 6 RMSD(585) = 2.3740 28 human serum albumin complexed with octadecanoic acid 1E7I 4496 585 1 29 recombinant human serum albumin 1UOR 4617 585 1 30 human serum albumin 1E78 4302 585 1 31 human serum albumin 1AO6 4600 585 1 32 human serum albumin 1BM0 4600 585 1 7 33 immunoglobulin 1IGY 10002 1294 4 34 immunoglobulin 1IGT 10196 1316 4 35 intact human IgG B12 1HZH 10355 1344 4 To quantify the similarity between the members of a class, for all sets, or subsets, i.e., for lysozyme and hemoglobins, the Root-Mean-Square Deviation (RMSD) has been calculated using the protein structure comparison service Fold at the European Bioinformatics Institute ( http://www.ebi.ac.uk/msd-srv/ssm ).
Adepth: New Representation and its implications for atomic depths of macromolecules.
(2013) Nucleic Acids Res 41
PubMed: 23609539 | PubMedCentral: PMC3692060 | DOI: 10.1093/nar/gkt299
The crystal structure of the antibody is represented by 1IGT ( 26 ) with vdw spheres and coloured atomic types: cyan for carbon, red for oxygen, blue for nitrogen and yellow for sulphur atoms.
The structural basis of antibody-antigen recognition.
(2013) Front Immunol 4
PubMed: 24115948 | PubMedCentral: PMC3792396 | DOI: 10.3389/fimmu.2013.00302
(A) The 3-D structure of an Ab molecule (PDB ID: 1IGT).
P-fimbriae in the presence of anti-PapA antibodies: new insight of antibodies action against pathogens.
PubMed: 24292100 | PubMedCentral: PMC3848023 | DOI: 10.1038/srep03393
To investigate, by modeling, the binding of two arms of an IgG molecule to helical and unwound P-fimbriae, we input the atomic models of P-fimbriae 29 , PapA dimer (pdb 2UY6), an IgG (pdb 1IGT), and a... IgG Fab with bound ligand (pdb 3HFM) into UCSF Chimera software 47 .
Conceptual modeling of anti-P-fimbriae antibody interactions on P-fimbriae In order to estimate both the maximum number of antibodies interacting with a single P-fimbrial shaft as well as the number of layers being clamped by an antibody, we used the P-fimbriae helical reconstruction map ( Fig. 6A 29 ;) and fitted a representative antibody class – immunoglobulin G (IgG) model (pdb 1IGT; Fig. 6B ) to a potential epitope on the shaft fimbrial subunits.
PubMed ID is not available.
Published in 2011
The dimensions of capping molecules are approximate and derived from RSCB protein databank by using software Jmol for insulin (PDB ID:1AI0), antibody (PDB ID:1IGT), i-motif DNA (PDB ID:1CN0) and doubl... stranded DNA (dsDNA, PDB ID:1BNA).
Publication Year: 2011
The Fab conformations in the solution structure of human immunoglobulin G4 (IgG4) restrict access to its Fc region: implications for functional activity.
(2014) J Biol Chem 289
PubMed: 24876381 | PubMedCentral: PMC4110284 | DOI: 10.1074/jbc.M114.572404
Three asymmetric structures include human IgG1 b12 (Protein Data Bank code 1HZH ( 37 )), murine IgG2a 231 (Protein Data Bank code 1IGT ( 53 )), and murine IgG1 61.1.3 (Protein Data Bank code 1IGY ( 54... )).
Publication Year: 2014
Immunoglobulin Structure Exhibits Control over CDR Motion.
(2011) Immunome Res 7
PubMed: 25191522 | PubMedCentral: PMC4151861 | DOI: null
Mean correlations of the motion derived from the first six normal modes with the total motion for (A) the entire structure, (B) the six CDR loops from chains A and B, (C) the six CDR loops from chains... C and D. 1IGT has 1316 residues in total.
(Inset) The CDRs from Fab1 are comprised of the variable loops in chains A and B, and the Fab2 CDRs are in chain C and D of 1IGT.
Physical Review Letters 2005 95 20 Enright MB Leitner DM Mass fractal dimension and the compactness of proteins Physical Review e 2005 71 21 Burioni R Cassi D Fontana MP Vulpiani A Vibrational thermodynamic instability of recursive networks Europhysics Letters 2002 58 806 810 22 Reuveni S Granek R Klafter J Proteins: Coexistence of stability and flexibility Physical Review Letters 2008 100 23 Reuveni S Granek R Klafter J Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure Proceedings of the National Academy of Sciences of the United States of America 2010 107 13696 13700 20639464 24 Leeuw M Reuveni S Klafter J Granek R Coexistence of flexibility and stability of proteins: an equation of state PLoS One 2009 4 e7296 19816577 25 Emekli U Schneidman-Duhovny D Wolfson HJ Nussinov R Haliloglu T automated prediction of hinges in protein structures Proteins 2008 70 1219 1227 17847101 26 Verner Schomaker Trueblood KN On the Rigid-Body Motion of Molecules in Crystals Acta Crystallography B 1968 24 63 76 Acta Crystallography B 27 Kuriyan J Weis WI Rigid protein motion as a model for crystallographic temperature factors Proc Natl Acad Sci U S A 1991 88 2773 2777 2011586 28 Song G Jernigan RL vGNM: a better model for understanding the dynamics of proteins in crystals J Mol Biol 2007 369 880 893 17451743 29 Linding R Jensen LJ Diella F Bork P Gibson TJ Russell RB Protein disorder prediction: implications for structural proteomics Structure 2003 11 1453 1459 14604535 30 Shimizu K Hirose S Noguchi T POODLE-S: web application for predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix Bioinformatics 2007 23 2337 2338 17599940 31 Janeway CA Travers P Walport M Shlomchik M Chapter 3–10 Immunobiology 2001 5th edition Garland Science 3 10 32 Dobbins SE Lesk VI Sternberg MJE Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking PNAS 2008 105 10390 10395 18641126 33 Bakan A Bahar I Computational generation inhibitor-bound conformers of P38 MAP kinase and comparison with experiments Proceedings of the Pacific Symposium on Biocomputing 2011 181 192 Figure 1 The structure of IgG (PDB structure 1IGT).
Mapping hydrophobicity on the protein molecular surface at atom-level resolution.
(2014) PLoS One 9
PubMed: 25462574 | PubMedCentral: PMC4252106 | DOI: 10.1371/journal.pone.0114042
Protein name PDB code Atoms Residues Chains 1 1 α lactalbumin 1A4V 1092 123 1 2 2 porcine β-lactoglobulin 1EXS 1248 160 1 3 bovine β-lactoglobulin 1BEB 2473 324 2 3 4 chicken e... g-white lysozyme 1LYZ 1001 129 1 5 turkey egg-white lysozyme 135L 994 129 1 6 hen egg-white lysozyme 2LYM 1001 129 1 7 triciclic lysozyme 2LZT 1001 129 1 8 mutant phage T4 lysozyme 1L35 1305 164 1 9 T4 lysozyme 1LYD 1309 164 1 4 10 ribonuclease-A 8RAT 951 124 1 11 ribonuclease-A 1RBX 956 124 1 12 bovine ribonuclease-A 3RN3 957 124 1 13 ribonuclease-A 1AFU 1894 248 2 5 14 human oxyhemoglobin 1HHO 2192 287 2 15 human carbonmonoxy hemoglobin 2HCO 2192 287 2 16 horse hemoglobin 2DHB 2201 287 2 17 human hemoglobin A 1BUW 4342 574 4 18 human hemoglobin 1Y4F 4368 574 4 19 hemoglobin mutant 1A01 4368 574 4 20 human hemoglobin 1Y4P 4376 574 4 21 hemoglobin mutant 1A00 4382 574 4 22 human hemoglobin 1Y46 4382 574 4 23 human deoxyhemoglobin 2HHB 4384 574 4 24 human hemoglobin 1Y4G 4366 574 4 25 hemoglobin mutant 1A0U 4386 574 4 26 hemoglobin mutant 1A0Z 4386 574 4 27 recombinant hemoglobin 1C7D 4396 576 3 6 28 human serum albumin complex with octadecanoic acid 1E7I 4496 585 1 29 recombinant human serum albumin 1UOR 4617 585 1 30 serum albumin 1E_78 4302 585 1 31 human serum albumin 1AO6 4600 585 1 32 human serum albumin 1BM0 4600 585 1 7 33 immunoglobulin 1IGY 10002 1294 4 34 immunoglobulin 1IGT 10196 1316 4 35 intact human IgG B12 1HZH 10355 1344 4 Note: The proteins marked in bold are model proteins and those in italics have been also used for the analysis of statistical strength.
Published in 2015
We estimated the corresponding linker sizes as 20, 10 and 5 nm, respectively, based on the structure of the IgG (PDB 1IGT 39 ).
Publication Year: 2015
Control of cytoplasmic dynein force production and processivity by its C-terminal domain.
(2015) Nat Commun 6
PubMed: 25670086 | PubMedCentral: PMC4339881 | DOI: 10.1038/ncomms7206
Three-dimensional model rendering and figure preparation Figures 1c,d and 2a were created with VMD 48 and The Persistence of Vision Raytracer (POV-Ray, http://www.povray.org/ ) using PDB entries 3VKH,... 3J2U, 1VF4 and 1IGT.
We chose 1IGT as an example to reflect the antibody dynamics by docking its three domains into each domain in the reconstruction.
Three available crystal structures of antibodies, 1IGT, 1HZH and 1IGY are very similar in the lengths of sequences.
By rigid-body docking a crystal structure (such as 1IGT 16 ) into the IPET reconstruction, the F c domain density map (criteria for domain identification described in supplemental information ) showed a near perfect match to that of its crystal structure in both of size and shape ( Fig. 2e left panel).
The F ab and F c domains of the mouse IgG2 antibody were therefore truncated from the crystal structure 1IGT 16 , and then the domains were rigid-body docked into a density map envelope by Chimera 59 .
Moreover, the resulting F ab or F c domains were obviously smaller in dimension than those of the crystal structures (PDB entry, 1IGT 16 , 1IGY 17 , 1HZH 18 ), or poor in resolution (failure to show the “ring” shape in domain F c ) and fuzzy, which was likely due to the flexibility of the domains in position and orientation.
e, Five snapshot images during TMD simulation illustrated the process of flexibly docking the crystal structure (PDB: 1IGT) into the IPET density map to achieve a new conformation of antibody.
The domain sizes and shapes were similar to those of the corresponding crystal structures (PDB entry, 1IGT 16 , 1IGY 17 , 1HZH 18 ), suggesting that antibody domains could directly be visualized by OpNS EM technique.
High-resolution template IgG structures like 1IGT.
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