PDBsum entry 1r3h

Immune system

PDB id: 1r3h

Contents

Protein chains

248 a.a. *

99 a.a. *

* Residue conservation analysis

PDB id:

1r3h

Name:

Immune system

Title:

Crystal structure of t10

Structure:

Mhc h2-tl-t10-129. Chain: a, c, e, g. Fragment: extracellular domain. Engineered: yes. Beta-2-microglobulin. Chain: b, d, f, h. Synonym: hdcma22p. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human. Organism_taxid: 9606. Gene: b2m.

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.231 R-free: 0.272

Authors:

M.G.Rudolph,I.A.Wilson

Key ref:

M.G.Rudolph et al. (2004). Combined pseudo-merohedral twinning, non-crystallographic symmetry and pseudo-translation in a monoclinic crystal form of the gammadelta T-cell ligand T10. Acta Crystallogr D Biol Crystallogr, 60, 656-664. PubMed id: 15039553 DOI: 10.1107/S0907444904002239

Date:

02-Oct-03 Release date: 30-Mar-04

Protein chains

Q31206  (Q31206_MOUSE) -  Ig-like domain-containing protein from Mus musculus

Seq: 406 a.a.

Struc: 248 a.a.

Protein chains

P61769  (B2MG_HUMAN) -  Beta-2-microglobulin from Homo sapiens

Seq: 119 a.a.

Struc: 99 a.a.

DOI no: 10.1107/S0907444904002239

Acta Crystallogr D Biol Crystallogr 60:656-664 (2004)

PubMed id: 15039553

Combined pseudo-merohedral twinning, non-crystallographic symmetry and pseudo-translation in a monoclinic crystal form of the gammadelta T-cell ligand T10.

M.G.Rudolph, C.Wingren, M.P.Crowley, Y.H.Chien, I.A.Wilson.

ABSTRACT

T10 is a non-classical class Ib-like major histocompatibility complex (MHC) cell-surface antigen which binds directly to certain gammadelta T-cell receptors in the absence of any exogenous and endogenous ligands, such as peculiar lipids or glycolipids. The crystal structure at 2.5 A resolution of murine T10 was determined by molecular replacement using data from an almost perfectly twinned monoclinic crystal. The space group is P2(1), with unit-cell parameters a = 78.2, b = 70.0, c = 139.2 A, beta = 106.8 degrees. Self-rotation function analysis and various intensity statistics revealed the presence of pseudo-merohedral twinning, but these tests underestimated the true twin fraction of alpha approximately 0.46. Native Patterson analyses pointed to the presence of pseudo-translation among the four molecules present in the asymmetric unit. Data analysis, structure determination and model refinement are discussed.

Selected figure(s)

Figure 1.
Figure 1 Detection and analysis of twinning. (a) Stereographic projection plot of the = 180° section of the self-rotation function of the native data set. The function was calculated with resolution limits of 15 and 3 Å, a Patterson integration radius of 27 Å and contoured at >40% of the maximum peak height using POLARRFN (Collaborative Computational Project, Number 4, 1994[Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.]). The data were reduced in P2, but the plot shows 222 symmetry, with one twofold axis ( = 0, at the centre) and the other twofold axes ( = 90°, at the perimeter) having equal heights. Detwinning of the data does not change the plot owing to the presence of a non-crystallographic twofold axis perpendicular to the b axis. (b) Cumulative distribution of Z = I/, where I is the intensity, for the acentric (continuous red line) and centric (dashed red line) T10 data. The theoretical distributions for untwinned data are shown as black lines. The sigmoidal shape of the distribution of the acentric reflections indicates potential twinning. (c) Estimation of the twin fraction by plotting the cumulative fractional intensity difference of acentric twin-related intensities, H = |I[1] - I[2]|/(I[1] + I[2]), as a function of H (Yeates, 1988[Yeates, T. O. (1988). Acta Cryst. A44, 142-144.]). The initial slope of the distribution is a measure of . The dotted lines represent the expected slopes for the indicated twin fractions. (d) Estimation of by a Britton plot (Britton, 1972[Britton, D. (1972). Acta Cryst. A28, 296-297.]; Fisher & Sweet, 1980[Fisher, R. G. & Sweet, R. M. (1980). Acta Cryst. A36, 755-760.]). The number of negative intensities after detwinning is plotted as a function of the assumed value of . An overestimation of will increase the number of negative intensities and the actual value of is extrapolated from this increase (dotted line). The line is a linear fit of the data with [189]>= 0.44 and intersects the x axis at [190][alpha] = 0.37.

Figure 4.
Figure 4 T10 structure and electron density. (a) The [A]-weighted 3F[o] - 2F[c] electron-density map contoured at 1.5 of the His31-Pro32 region in the [2]m molecule of T10 shows the presence of a cis-peptide bond which was not modelled in the lower resolution T22 structure. (b) Superposition of the ligand-binding site of T10 (flesh coloured) and T22 (pale blue) shows that both MHC-like molecules are very similar. (c) Ribbon representation of the T10 model. The -strands in the left panel are coloured blue, -helices red and loop regions grey. The MHC-like domains are labelled. The loop region in T10, which replaces the first half of the [2]-helical segments, was not visible in the electron-density maps and is drawn as a dashed line. The right panel shows an overlay of the four molecules in the asymmetric unit. Each heterodimer is individually coloured.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 656-664) copyright 2004.

Figures were selected by an automated process.