Citations in PubMed

Primary Citation PubMed: 16611889 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 4

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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The crystal structure of the SV40 T-antigen origin binding domain in complex with DNA.

(2007) PLoS Biol 5

PubMed: 17253903 | PubMedCentral: PMC1779811 | DOI: 10.1371/journal.pbio.0050023

Accession Numbers Protein Data Bank ( http://www.rcsb.org/pdb ) accession numbers for the coordinates for the T-ag obd co-structure and disulfide-linked dimer are 2NTC and 2IF9, respectively, and for ... he T-ag obd residues that comprise the protein–protein interface in the spiral hexamer, 2FUF.

Publication Year: 2007


Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.

(2010) Open Biochem J 4

PubMed: 21293729 | PubMedCentral: PMC3032220 | DOI: 10.2174/1874091X01004010083

NMR X-ray PDB entry Chain Number of models PDB entry Chain Resolution (Å) 1 2JQX A 1 1D8C A 2.00 2 1EZO A 10 1ANF A 1.67 3 1AH2 A 18 1IAV A 1.80 4 1TR4 A 20 1UOH A 2.00 5 1BXL A 1 1MAZ A 2.20 ... 2GPQ A 10 1IPB A 2.00 7 1A23 A 1 1A2J A 2.00 8 1MM4 A 20 1THQ A 1.90 9 1GGR A 3 2F3G B 2.13 10 1CRP A 20 1GNP A 2.70 11 1OCA A 20 1W8L A 1.80 12 1NMV A 10 1PIN A 1.35 13 1AX3 A 16 1GPR A 1.90 14 1DF3 A 10 1JV4 A 1.75 15 1B6F A 23 1BV1 A 2.00 16 1EQ0 A 20 1DY3 A 2.00 17 1BVH A 15 1DG9 A 1.90 18 1RCH A 8 1RDD A 2.80 19 6I1B A 1 1I1B A 2.00 20 1BA9 A 36 1MFM A 1.02 21 1XPW A 20 1TVG A 1.60 22 1FXT A 1 1FZY B 1.90 23 1JOK A 1 1SNO A 1.70 24 1CFC A 25 1A29 A 2.74 25 1ORM A 20 1QJ8 A 1.90 26 1PFL A 20 1FIK A 2.30 27 1BLR A 22 1CBQ A 2.20 28 2P3M A 20 2VBS A 3.00 29 1JJJ A 20 1B56 A 2.05 30 1JBH A 20 1CRB A 2.10 31 1TBD A 1 2FUF A 1.45 32 1AEL A 20 1ICM A 1.50 33 1A63 A 10 1A62 A 1.55 34 1IY3 A 1 1IWT A 1.40 35 1CYL A 20 1HIK A 2.60 36 1CEY A 46 1CHN A 1.76 37 2JU3 A 10 1LFO A 2.30 38 1FR0 A 30 1A0B A 2.06 39 1GIO A 10 1AGI A 1.50 40 2PRF A 19 1PRQ A 2.50 41 1MVG A 10 1TVQ A 2.00 42 2AAS A 32 1AQP A 2.00 43 1FSP A 20 1NAT A 2.45 44 1PIR A 1 1P2P A 2.60 45 1IT4 A 1 1FAZ A 1.40 46 1KLV A 20 1GNU A 1.75 47 2JN8 A 20 2ES9 A 2.00 48 1SVQ A 20 1SVY A 1.75 49 1K19 A 20 1KX8 A 2.80 50 1BC4 A 15 1KM8 A 1.90 51 1BNR A 20 1YVS A 2.20 52 1A67 A 16 1CEW I 2.00 53 2NLN A 20 1OMD A 1.85 54 1F40 A 10 1FKB A 1.70 55 1MPH A 50 1BTN A 2.00 56 1N5H A 15 1PFP A 2.30 57 1IYY A 24 1BU4 A 1.90 58 2CZN A 38 2CWR A 1.70 59 1N7T A 20 2H3L B 1.00 60 2EVN A 20 2IL4 A 2.05 61 1GO0 A 10 1H7M A 1.96 62 1M42 A 1 2C9Q A 1.60 63 1IIY A 1 3EZM A 1.50 64 1JNJ A 20 1LDS A 1.80 65 1BEG A 18 1BEO A 2.20 66 1C15 A 16 1CY5 A 1.30 67 1BMW A 38 1WHO A 1.90 68 2JMV A 20 2QSK A 1.00 69 1AFH A 15 1FK0 A 1.80 70 3HSF A 30 2HTS A 1.83 71 1PQX A 10 2FFM A 2.51 72 1L8Y A 30 2HDZ A 2.00 73 2CKU A 15 2CG6 A 1.55 74 1A2S A 1 1CTJ A 1.10 75 1ACA A 20 1HB6 A 2.00 76 1GGR B 3 1POH A 2.00 77 1ACP A 2 1T8K A 1.10 78 1D3Z A 10 1AAR B 2.30 79 1RQS A 20 1CTF A 1.70 80 2AIT A 9 1HOE A 2.00 81 1FD8 A 1 1CC7 A 1.20 82 1K3G A 30 1C75 A 0.97 83 2ORC A 32 1ORC A 1.54 84 1HFG A 1 2FHT A 1.70 85 1ZUG A 20 2CRO A 2.35 86 1BQT A 6 1GZR B 2.0 87 3MEF A 16 1MJC A 2.00 88 2BTT A 20 1RUW A 1.80 89 1QQV A 1 1YU5 X 1.40 90 1LQH A 1 2ASC A 1.10 91 1IJC A 20 1F94 A 0.97 92 1AEY A 15 1SHG A 1.80 93 1ERA A 1 3EBX A 1.40 94 1ROF A 10 1VJW A 1.75 95 1JV8 A 23 1BPI A 1.09 96 1H0T B 40 1LP1 A 2.30 97 1KUN A 20 1KNT A 1.60 98 1GB1 A 60 1PGA A 2.07 99 1BFY A 20 1FHH A 1.50 100 1MBE A 1 1GUU A 1.60 101 1FDM 20 2C0W A 3.20 102 1CCM A 8 1CBN A 0.83 103 1PJF A 27 1QL1 A 3.10 104 1HEV A 6 1Q9B A 1.50 105 1ERC A 20 2ERL A 1.00 106 1KX6 A 20 1GCN A 3.00 107 1CIR B 20 1CIQ B 2.20 108 1V6R A 20 1EDN A 2.18 109 1XGA A 35 1NOT A 1.20 Table 2 Mean RMDS and RMDS 100 Values (Standard Deviations in Parenthesis) Calculated for the Superposed Equivalent X-Ray Protein Structure and NMR Models.

Publication Year: 2010


Structure-based design of a disulfide-linked oligomeric form of the simian virus 40 (SV40) large T antigen DNA-binding domain.

(2011) Acta Crystallogr D Biol Crystallogr 67

PubMed: 21636896 | PubMedCentral: PMC3107053 | DOI: 10.1107/S0907444911014302

The C-terminal portion of T-­ag OBD has been shown to adopt alternate conformations in different structures of T-ag OBD (PDB entries 1tbd , 2fuf , 2ntc , 2if9 , 2ipr , 2itj , 2itl and 2nl8 ; M... inke et al. , 2006 ▶ , 2007 ▶ ; Luo et al. , 1996 ▶ ; Bochkareva et al. , 2006 ▶ ), indicating that it is also a region of high flexibility.

Our structure of the T-ag OBD (PDB entry 2fuf ) crystallized in a hexagonal space group in which the protein formed a helical filament in the crystal with six monomers per turn (Meinke et al. , 2006 ▶ ).

We used SSBOND to analyze the protein–protein interface of the SV40 T-ag OBD open-ring hexamer crystal structure (PDB entry 2fuf ).

The structure of the triple mutant was solved by molecular replace­ment using apo T-ag OBD coordinates as a search model (PDB entry 2fuf ) and the program Phaser (McCoy et al. , 2005 ▶ ).

This crystal structure of wt SV40 T-ag OBD (PDB entry 2fuf ) has one monomer in the asymmetric unit and six monomers per turn (Figs. 1 ▶ a and 1 ▶ b ).

Publication Year: 2011


Insights into the initiation of JC virus DNA replication derived from the crystal structure of the T-antigen origin binding domain.

(2014) PLoS Pathog 10

PubMed: 24586168 | PubMedCentral: PMC3930596 | DOI: 10.1371/journal.ppat.1003966

Schematics depicting the crystallographic spirals formed by the JCV T-ag OBD and the SV40 T-ag OBD (PDB entry 2FUF) are presented in Fig. 8C (left and right; respectively).

The previously solved structures used in the molecular modeling discussed herein are the apo SV40 T-ag OBD and DNA bound SV40 T-ag OBD (RCSB PDB codes 2FUF, and 2NTC).

The program PyMOD [62] was used to generate a search model from the coordinates of the SV40 T-antigen OBD crystal structure (PDB ID = 2FUF) [63] .

Publication Year: 2014