Citations in PubMed

Primary Citation PubMed: 12004122 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 14

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Prediction of transmembrane helix orientation in polytopic membrane proteins.

(2006) BMC Struct Biol 6

PubMed: 16792816 | PubMedCentral: PMC1540425 | DOI: 10.1186/1472-6807-6-13

The PDB names for the protein structures used: 1C3W , 1E12 , 1EHK , 1EUL , 1FX8 , 1H2S , 1IWG , 1J4N , 1JB0 , 1K4C , 1KB9 , 1KF6 , 1KPL , 1KQF , 1L7V , 1L9H , 1M3X , 1M56 , 1MSL , 1NEK , 1OCR , 1OKC ,... 1PP9 , 1PV6 , 1PW4 , 1Q16 , 1QLA , 1Q90 , 1RH5 .

Publication Year: 2006


Quaternary structure predictions of transmembrane proteins starting from the monomer: a docking-based approach.

(2006) BMC Bioinformatics 7

PubMed: 16836758 | PubMedCentral: PMC1590055 | DOI: 10.1186/1471-2105-7-340

Structures f C α -RMSD i BtuCD 1L7V 3.2 Dimer a A-Bs1678 g 0.63 BRD* 1BRR 2.9 Trimer b A-Bs162-Cs14 1.04 AmtB 1U77 1.35 Trimer a A-Bs7-Cs1 1.17 b A-Bs7-Cs1 0.83 c A-Bs1-Cs1 0.75 AcrB 1IWG 3.5 ... rimer a A-Bs4-Cs1 2.78 b A-Bs4-Cs1 1.56 c A-Bs1-Cs1 1.64 KcsA* 1BL8 3.3 Tetramer a A-Bs1-Cs500-Ds2 h 1.79 b A-Bs1-Cs1-Ds2 2.45 c A-Bs2-Cs1-Ds2 2.77 AQP1 1J4N 2.2 Tetramer a A-Bs2-Cs1-Ds1 1.31 b A-Bs1-Cs2-Ds1 1.71 c A-Bs2-Cs4-Ds1 1.37 GlpF 1FX8 2.2 Tetramer a A-Bs2-Cs1-Ds1 1.11 b A-Bs1-Cs2-Ds1 1.16 c A-Bs2-Cs2-Ds1 1.39 KirBac1 1P7B 3.65 Tetramer a A-Bs3-Cs1-Ds1 1.53 b A-Bs3-Cs1-Ds3 1.47 c A-Bs2-Cs1-Ds1 1.80 MscL* 1MSL 3.5 Pentamer a A-Bs5-Cs1-Ds4-Es6 3.45 b A-Bs5-Cs3-Ds2-Es1 2.83 c A-Bs8-Cs1-Ds1-Es6 2.47 MscS* 1MXM 3.9 Eptamer a A-Bs3-Cs3-Ds3-Es1-Fs1-Gs1 2.21 b A-Bs3-Cs3-Ds1-Es165-Fs3-Gs1 11.30 c A-Bs3-Cs1-Ds1-Es6-Fs1-Gs1 2.06 a Abbreviated name of the membrane proteins subjected to the benchmarks.

They include a dimer, i.e. the membrane spanning region of the BtuCD Vitamin B12 Transporter (648 amino acids, PDB code: 1L7V ) [ 28 ]; trimers like the AmtB ammonia channel (1146 amino acids, PDB code: 1U77 ) [ 29 ] and the AcrB bacterial multi-drug efflux transporter (3108 amino acids, PDB code: 1IWG ); and tetramers like the AQP1 aquaporin water channel (996 amino acids, PDB code: 1J4N ) [ 30 ], the GlpF glycerol facilitator channel (1016 amino acids, PDB code: 1FX8 ) [ 31 ], and the KirBac1 Inward-Rectifier Potassium channel (1032 amino acids, PDB code: 1P7B ) [ 32 ].

Figure 10 Superimposition between native (green color) and the best native-like (violet color) oligomeric structures of: (a) AQP1 (PDB code: 1J4N ; C α -RMSD = 1.31 Å; best predicted tetramer: A-Bs2-Cs1-Ds1), (b) GlpF (PDB code: 1FX8 ; C α -RMSD = 1.11 Å; best predicted tetramer: A-Bs2-Cs1-Ds1), (c) KirBac1 (PDB code: 1P7B ; C α -RMSD = 1.47 Å; best predicted tetramer: A-Bs3-Cs1-Ds3), (d) AmtB (PDB code: 1U77 ; C α -RMSD = 0.75 Å; best predicted trimer: A-Bs1-Cs1), (e) AcrB (PDB code: 1IGW ; C α -RMSD = 1.56 Å; best predicted trimer: A-Bs4-Cs1), and (f) BtuCD (PDB code: 1L7V ; C α -RMSD = 0.63 Å).

Publication Year: 2006


COPII-dependent export of cystic fibrosis transmembrane conductance regulator from the ER uses a di-acidic exit code.

(2004) J Cell Biol 167

PubMed: 15479737 | PubMedCentral: PMC2172508 | DOI: 10.1083/jcb.200401035

pdb) is oriented to show its structural homology with the NBD1 structural domain of the bacterial ABC transporter BtuCD (1L7V.

The Sec24/NBD1/Sec23/Sar1/BtuCD complex model was built from the Sec24/NBD1/Sec23/Sar1 model and BtuCD (1L7V.

Publication Year: 2004


Modeling kinetics of subcellular disposition of chemicals.

(2009) Chem Rev 109

PubMed: 19265398 | PubMedCentral: PMC2682929 | DOI: 10.1021/cr030440j

The latter category includes multidrug transporter Sav1866 from Staphylococcus aureus ( 1171 , 1172 ) (Protein Data Bank (PDB)( 1173 ) files 2ONJ , shown in Figure 9 , and 2HYD ); molybdate/tungstate ... ransporter ModBC-A from Archaeoglobus fulgidus ( 1174 ) ( 2ONK ), vitamin B12 permease BtuCD from Escherichia coli ( 1163 ) ( 1L7V ), putative metal-chelate importer HI147Q/71 from Haemophilus influenzae ( 1175 ) ( 2NQ2 ); multidrug transporter MsbA from E. coli ( 3B5W ), Vibrio cholerae ( 3B5X ), Salmonella typhimurium ( 3B5Y , 3B5Z , 3B60 ), and multidrug transporter EmrE from E. coli ( 1176 ) ( 3B5W , 3B61 , 3B62 ).

Publication Year: 2009


The Membrane Protein Data Bank.

(2006) Cell Mol Life Sci 63

PubMed: 16314922 | PubMedCentral: PMC2792347 | DOI: 10.1007/s00018-005-5350-6

D 2 O, used in the crystallization of BtuCD (1L7V), is another example.

Publication Year: 2006


MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane.

(2010) BMC Bioinformatics 11

PubMed: 20565847 | PubMedCentral: PMC2904353 | DOI: 10.1186/1471-2105-11-333

Assessing quality of protein structures Agreement between predicted and structurally derived accessibility was tested on six PDB-structures downloaded from PDB: 1S7B , 2F2M , 1JSQ , 1PF4 , 1Z2R , 1L7V... and 2HYD .

Publication Year: 2010


Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function.

(2010) BMC Bioinformatics 11

PubMed: 20102603 | PubMedCentral: PMC3098086 | DOI: 10.1186/1471-2105-11-52

Although no crystal structures have been determined for UrtBC, two structures from homologous transporters in the CL0142 clan have been published: the B12 transporter permease/ATPase complex BtuCD fro... E. coli [PDB: 1L7V ] [ 12 ], and the unknown specificity permease/ATPase complex HI1471/HI1470 from Haemophilus influenzae [PDB: 2NQ2 ] [ 13 ].

Right: Mapping onto the "outward-open" structure of BtuC [PDB: 1L7V ][ 12 ].

Publication Year: 2010


The conformational transition pathways of ATP-binding cassette transporter BtuCD revealed by targeted molecular dynamics simulation.

(2012) PLoS One 7

PubMed: 22272354 | PubMedCentral: PMC3260306 | DOI: 10.1371/journal.pone.0030465

The BtuCD protein (PDBID: 1L7V) was inserted into POPE (palmitoyl-oleoyl phosphatidyl-ethanolamine) bilayer by “shrinking” method [44] .

The missing fragments in HI1470/1 crystal structure, including the N-terminus of TM1 helix (residue 1 to 4), the extracellular loop 1 (ECL1, residue 20 to 56) and the N-terminus of TM5 helix (residue 140 to 146), were patched up by the corresponding fragments in the BtuCD crystal structure (PDBID: 1L7V).

(a) The ribbon diagram of the crystal structure of BtuCD (PDBID: 1L7V) in an outward-facing conformation, and (b) the close-up view of its translocation pathway, where the hydrophobic residues are shown in stick model.

Publication Year: 2012


Structural insights into the regulation of cohesion establishment by Wpl1.

(2013) EMBO J 32

PubMed: 23395900 | PubMedCentral: PMC3590988 | DOI: 10.1038/emboj.2013.16

( B ) Superimposition of ScSmc1 with the ATPase domain of Rad50 (pdb i.d. 3qkt) and BtuD (pdb i.d. 1l7v).

Publication Year: 2013


Structural genomics of membrane proteins.

(2004) Genome Biol 5

PubMed: 15059248 | PubMedCentral: PMC395774 | DOI: 10.1186/gb-2004-5-4-215

(a) Side-view of BtuCD Vitamin B12 Transporter [ 51 ] containing an α-helical transmembrane region (PDB accession code 1L7V); and (b) side-view of FecA Ferric Citrate Uptake Receptor [ 52 ] fe... turing a β-barrel transmembrane region (PDB accession code 1KMO).

Publication Year: 2004


Structural diversity of ABC transporters.

(2014) J Gen Physiol 143

PubMed: 24638992 | PubMedCentral: PMC3971661 | DOI: 10.1085/jgp.201411164

Reference Type I importers Molybdate transporter ModB 2 C 2 -A complex ( Archaeoglobus fulgidus ) Inward-facing conformation, with SBP bound Mg 2+ , PO 4 3- , WoO 4 2− 3.10 2ONK Hollenstein et... al., 2007 ModBC ( Methanosarcina acetivorans ) Inward-facing conformation, without SBP bound, in a trans-inhibited state Mg 2+ , WoO 4 2− 3.00 3D31 Gerber et al., 2008 MalFGK 2 -MBP maltose uptake transporter ( E. coli ) Outward-facing conformation stabilized by a mutation in the NBDs (MalK E159Q), with MBP Maltose, ATP 2.80 2R6G Oldham et al., 2007 MalFGK 2 maltose uptake transporter ( E. coli ) TM helix 1 deleted, in inward-facing conformation, in resting state, without MBP — 4.50 3FH6 Khare et al., 2009 MalFGK 2 -MBP maltose uptake transporter ( E. coli ) Pre-translocation intermediate state, with mutations in MBP (G69C/S337C) that stabilize the substrate-bound closed conformation by a cross-link AMP-PNP, Mg 2+ , maltose 2.90 3PUZ Oldham and Chen, 2011a Outward-facing conformation state, with MBP AMP-PNP, Mg 2+ , maltose 3.10 3PUY Pre-translocation intermediate state, with mutations in MBP (G69C/S337C) that stabilize the substrate-bound closed conformation by a cross-link Maltose 3.10 3PV0 MalFGK 2 -MBP maltose uptake transporter ( E. coli ) Outward-facing conformation, with MBP AMP-PNP, Mg 2+ , maltose 2.20 3RLF Oldham and Chen, 2011b Outward-facing conformation, with MBP ADP · VO 4 3− , Mg 2+ , maltose 2.40 3PUV Outward-facing conformation, with MBP ADP · AlF 4 − , Mg 2+ , maltose 2.30 3PUW Outward-facing conformation, with MBP ADP · BeF 3 − , Mg 2+ , maltose 2.30 3PUX MalFGK 2 -MBP maltose uptake transporter ( E. coli ) Complex with its regulatory protein EIIAglc, inward-facing conformation — 3.91 4JBW Chen et al., 2013 MalFGK 2 -MBP maltose uptake transporter ( E. coli ) Outward-facing conformation, with MBP Maltoheptaose 2.90 4KHZ Oldham et al., 2013 Outward-facing conformation, with MBP ANP, α- d -glycose 2.38 4KI0 MetNI methionine uptake transporter ( E. coli ) Inward-facing conformation — 3.70 3DHW Kadaba et al., 2008 Inward-facing conformation, at higher resolution (detergent Cymal5) ADP 2.90 3TUI Johnson et al., 2012 Inward-facing conformation, C2 domains repositioned (detergent decylmaltoside) — 4.00 3TUJ Type II importers BtuC 2 D 2 vitamin B 12 transporter ( E. coli ) Outward-facing conformation, no SBP bound V 4 O 12 4− 3.20 1L7V Locher et al., 2002 BtuC 2 D 2 -F complex ( E. coli ) BtuC in asymmetric conformation.

Structures have been determined for an outward-open, occluded nucleotide-bound, and closed ATP-free asymmetric transporter (Protein Data Bank accession nos.: 1L7V , 4DBL , and 2QI9 ; see Table 1 for details of all available structures of ABC transporters).

Publication Year: 2014


High-resolution modeling of transmembrane helical protein structures from distant homologues.

(2014) PLoS Comput Biol 10

PubMed: 24854015 | PubMedCentral: PMC4031050 | DOI: 10.1371/journal.pcbi.1003636

non-GPCRs: Aquaporins (1J4N, 3GD8), Glycerol channel (1FX8), Formate channel (3KLY), Arginine antiporter (3L1L), Lactose Permease (2CFQ), EmrD multidrug transporter (2GPF), E. coli GlpG rhomboid famil... intramembrane protease (2IC8), GlpG, Rhomboid Peptidase from Haemophilus influenzae (2NR9), E. coli BtuCD protein, an ABC transporter mediating vitamin B12 uptake (1L7V), putative metal-chelate-type adenosine triphosphate (ATP)-binding cassette (ABC) transporter from Haemophilus influenzae (2NQ2), E. coli Ammonia Channel AmtB (1U7G), Ammonium Transporter Amt-1 from Archaeoglobus fulgidus (2B2H), Rhesus protein Rh50 from Nitrosomonas europaea (3B9W), ECF-type riboflavin transporter from Staphylococcus aureus (3P5N), thiamine-specific S-component ThiT ECF-type transporter from Lactococcus lactis (3RLB), apo-ApcT, a proton-coupled broad-specificity amino acid transporter (3GIA), Glu-GABA antiporter GadC, a member of the amino-acid-polyamine-organocation superfamily of membrane transporters (4DJK), Cyanobacterial Cl−/H+ antiporter (3ND0), eukaryotic CLC transporter (3ORG), Protein translocases SecY (1RH5, 2ZJS), Energy-coupling factor transporter EcfA (4HZU), Sodium/calcium exchanger (3V5U), Proton/calcium exchanger (4KPP), Proton-driven MATE exporter (3VVO), Sodium/drug antiporter NorM (3MKT), Rhesus Glycoprotein RhCG (3HD6).

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4360534

Locher K.P , Lee A.T , Rees D.C , 2002 , Bacterial ABC Transporter Involved in B12 Uptake , 1L7V ; http://dx.doi.org/10.2210/pdb1L7V/pdb , Publicly available at the RCSB Protein Data Bank.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4379700

Hopf et al. have predicted [ 19 ] the unknown structures of ADR1_HUMAN with structural similarity to Bacteriorhodopsin (Pfam: PF01036, PDB-Id: 3hao) and LIVH_ECOLI with structural similarity to permea... e protein BtuC (Pfam: PF01032, PF00005, PDB-Id: 1l7v) in their work.

Publication Year: 2015