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- PDB-4g43: Structure of the chicken MHC class I molecule BF2*0401 complexed ... -

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Basic information

Entry
Database: PDB / ID: 4g43
TitleStructure of the chicken MHC class I molecule BF2*0401 complexed to P5E
Components
  • 8-MERIC PEPTIDE P5E
  • Beta-2 microglobulin
  • MHC class I alpha chain 2
KeywordsIMMUNE SYSTEM / MHC I complex / narrow binding groove
Function / homology
Function and homology information


MHC class I protein binding, via antigen binding groove / ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular response to iron ion ...MHC class I protein binding, via antigen binding groove / ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / transcription coregulator activity / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / regulation of DNA-templated transcription / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular space / extracellular region / nucleus / metal ion binding / cytosol
Similarity search - Function
TAF15/EWS/TLS family / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / : / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 ...TAF15/EWS/TLS family / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / : / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / RNA-binding domain superfamily / : / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Nucleotide-binding alpha-beta plait domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I alpha chain 2 / Beta-2-microglobulin / FUS/TLS
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.803 Å
AuthorsZhang, J. / Chen, Y. / Qi, J. / Gao, F. / Liu, J. / Kaufman, J. / Xia, C. / Gao, G.F.
CitationJournal: J.Immunol. / Year: 2012
Title: Narrow Groove and Restricted Anchors of MHC Class I Molecule BF2*0401 Plus Peptide Transporter Restriction Can Explain Disease Susceptibility of B4 Chickens.
Authors: Zhang, J. / Chen, Y. / Qi, J. / Gao, F. / Liu, Y. / Liu, J. / Zhou, X. / Kaufman, J. / Xia, C. / Gao, G.F.
History
DepositionJul 16, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I alpha chain 2
B: Beta-2 microglobulin
C: 8-MERIC PEPTIDE P5E
D: MHC class I alpha chain 2
E: Beta-2 microglobulin
F: 8-MERIC PEPTIDE P5E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8137
Polymers88,6956
Non-polymers1181
Water10,917606
1
A: MHC class I alpha chain 2
B: Beta-2 microglobulin
C: 8-MERIC PEPTIDE P5E


Theoretical massNumber of molelcules
Total (without water)44,3473
Polymers44,3473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-16 kcal/mol
Surface area18380 Å2
MethodPISA
2
D: MHC class I alpha chain 2
E: Beta-2 microglobulin
F: 8-MERIC PEPTIDE P5E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4664
Polymers44,3473
Non-polymers1181
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-11 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.920, 40.241, 132.622
Angle α, β, γ (deg.)90.00, 120.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MHC class I alpha chain 2 / MHC class I glycoprotein / MHC class I molecule


Mass: 31853.465 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 22-291 / Mutation: D244E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: O46790
#2: Protein Beta-2 microglobulin


Mass: 11469.888 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P21611
#3: Protein/peptide 8-MERIC PEPTIDE P5E


Mass: 1024.104 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in Gallus. / Source: (synth.) Gallus gallus (chicken) / References: UniProt: Q6J4Y8*PLUS
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 606 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% MPD, 20% PEG 6000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Dec 8, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→41.306 Å / Num. all: 92269 / Num. obs: 69202 / % possible obs: 75 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.1849 / Mean I/σ(I) obs: 7.5 / Num. unique all: 92269 / Rsym value: 0.279 / % possible all: 75

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.803→41.306 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 3498 5.05 %RANDOM
Rwork0.1832 ---
all0.2179 92269 --
obs0.1849 69202 97.47 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.091 Å2 / ksol: 0.422 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.3 Å20 Å20.5617 Å2
2--3.5791 Å20 Å2
3----1.2791 Å2
Refinement stepCycle: LAST / Resolution: 1.803→41.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6107 0 8 606 6721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056297
X-RAY DIFFRACTIONf_angle_d0.9758546
X-RAY DIFFRACTIONf_dihedral_angle_d15.5062300
X-RAY DIFFRACTIONf_chiral_restr0.072862
X-RAY DIFFRACTIONf_plane_restr0.0041120
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8031-1.82780.30271160.2245228683
1.8278-1.85390.2581330.2168240393
1.8539-1.88160.25411230.1985248694
1.8816-1.9110.22771250.1953262596
1.911-1.94230.20551230.1913253995
1.9423-1.97580.23661560.178252696
1.9758-2.01170.20451320.1731264297
2.0117-2.05040.20851430.1681254297
2.0504-2.09230.21751430.1738262797
2.0923-2.13770.21881280.1828264798
2.1377-2.18750.24371230.183261098
2.1875-2.24220.2231690.1816266199
2.2422-2.30280.21271270.1808261699
2.3028-2.37050.20781610.1891267799
2.3705-2.44710.251310.1801265099
2.4471-2.53450.19541350.1826269599
2.5345-2.6360.22481240.1862686100
2.636-2.75590.23641470.19922672100
2.7559-2.90120.22641570.19252709100
2.9012-3.08290.20881650.18692678100
3.0829-3.32080.19271520.18262707100
3.3208-3.65480.19491560.17332714100
3.6548-4.18320.19841400.16532718100
4.1832-5.26870.19381280.1552763100
5.2687-41.31670.26871610.225282599
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.75180.1587-0.32440.1590.1080.5650.03080.05410.02850.0044-0.02450.0601-0.03560.0329-0.01330.0769-0.00580.00010.02750.01070.079530.0251-19.056324.7704
20.650.1346-0.03560.3276-0.22660.1225-0.02390.04120.0802-0.0185-0.01020.0564-0.01310.1507-0.00610.0875-0.0191-0.01290.05120.00860.109330.5783-12.340717.729
30.1859-0.4256-0.04940.40710.02590.3876-0.0692-0.00950.00870.00370.0050.10080.1035-0.1652-0.01510.1396-0.0563-0.03580.15380.01410.145813.5696-12.4666-6.1499
40.1208-0.08820.13690.0068-0.05620.064-0.02230.0994-0.0551-0.05810.01430.01250.0335-0.11740.0040.1651-0.03250.00530.1281-0.03460.105317.409-25.73192.9912
50.0449-0.03330.01590.0419-0.05590.0621-0.2304-0.27-0.13370.05530.32340.08210.0944-0.2586-0.00930.218-0.1926-0.0621-0.5553-0.3442-0.062414.9072-34.43810.398
6-0.0129-0.0164-0.00680.0821-0.01740.069-0.00840.04940.0262-0.146-0.0495-0.09810.09530.08-0.00640.15450.0260.02440.0838-0.00290.127722.0231-24.380315.2783
70.02280.0746-0.03040.032-0.01440.007-0.04260.0543-0.0091-0.01930.0796-0.1264-0.0240.0555-0.00470.166-0.0331-0.00420.0961-0.03370.122121.8849-29.16676.7438
80.0556-0.06290.05320.0981-0.00710.0329-0.0697-0.0205-0.0412-0.07630.06830.01240.0474-0.13120.01170.1841-0.0779-0.00590.1709-0.05620.12099.7461-33.56787.7486
90.0067-0.0140.00760.0091-0.00820.00820.0404-0.12020.1032-0.1304-0.20910.0546-0.0336-0.256800.1839-0.0408-0.05160.2207-0.03760.19369.8481-29.4434-0.2732
100.7853-0.00970.27960.48570.18190.81180.0739-0.1992-0.04740.0317-0.11890.03890.0509-0.1333-0.10950.0605-0.06480.01220.16990.02930.0738-29.3036-41.940837.0784
110.08530.0083-0.0050.12450.01210.02160.01760.0416-0.06270.00440.0277-0.0538-0.0063-0.01380.00690.077-0.0059-0.00590.09440.01480.0828-5.6218-41.755631.2336
120.2182-0.0498-0.18650.37610.07150.4089-0.0293-0.0854-0.08370.03680.0350.02480.07540.04630.00110.05910.01040.0020.04850.01750.08267.4197-41.179443.4721
130.1268-0.03530.0970.04490.07110.0640.0027-0.05320.004-0.0608-0.0354-0.0510.0322-0.0407-0.00470.0847-0.00980.00260.07220.00720.0893-4.6167-28.655843.2957
140.00590.0278-0.0103-0.0101-0.0014-0.00560.026-0.1714-0.0059-0.0321-0.040.0062-0.0981-0.182100.1219-0.0245-0.00190.1853-0.01520.1581-14.882-24.040148.1748
150.0051-0.01890.01850.0262-0.01320.00320.07020.01670.0927-0.17110.06030.0315-0.2594-0.002300.2316-0.00120.00180.14030.02640.2164-8.4983-16.838841.6463
16-0.0020.0082-0.00470.0065-0.0067-0.0085-0.01110.04530.0302-0.1578-0.1099-0.0632-0.2697-0.0385-00.2505-0.04170.05460.19930.030.1529-18.6823-33.55140.0411
17-0.00820.0436-0.10150.01910.15810.0425-0.0524-0.04780.1136-0.2552-0.00820.09620.0416-0.0817-0.0020.1049-0.018-0.00890.14170.02410.124-13.1084-31.669742.33
180.009-0.0046-0.02130.06390.01190.0220.082-0.21970.0850.0479-0.097-0.0146-0.1602-0.1107-0.00450.136-0.02830.01370.1791-0.02440.1093-8.2044-21.511651.6984
190.0109-0.03440.01820.00970.00570.0255-0.0074-0.1724-0.00020.17110.0466-0.08950.29870.01400.12980.0004-0.02430.13770.00220.1244-0.5317-25.439150.131
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:134)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 135:193)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 194:272)
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 1:29)
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 30:45)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 46:60)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 61:70)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 71:89)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 90:97)
10X-RAY DIFFRACTION10CHAIN D AND (RESSEQ 1:159)
11X-RAY DIFFRACTION11CHAIN D AND (RESSEQ 160:193)
12X-RAY DIFFRACTION12CHAIN D AND (RESSEQ 194:272)
13X-RAY DIFFRACTION13CHAIN E AND (RESSEQ 1:29)
14X-RAY DIFFRACTION14CHAIN E AND (RESSEQ 30:40)
15X-RAY DIFFRACTION15CHAIN E AND (RESSEQ 41:50)
16X-RAY DIFFRACTION16CHAIN E AND (RESSEQ 51:55)
17X-RAY DIFFRACTION17CHAIN E AND (RESSEQ 56:70)
18X-RAY DIFFRACTION18CHAIN E AND (RESSEQ 71:89)
19X-RAY DIFFRACTION19CHAIN E AND (RESSEQ 90:97)

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