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- PDB-7zqi: MHC class I from a wild bird in complex with a nonameric peptide P2 -

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Basic information

Entry
Database: PDB / ID: 7zqi
TitleMHC class I from a wild bird in complex with a nonameric peptide P2
Components
  • Beta-2-microglobulin
  • Inosine monophosphate dehydrogenase-related protein
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Major Histocompatibility Complex Class I / Acrocephalus arundinaceus / antigen presentation / cell-surface receptor / nonameric peptide from Vibrio
Function / homology
Function and homology information


response to metal ion / antigen processing and presentation of peptide antigen via MHC class I / MHC class I protein complex / immune response / external side of plasma membrane / extracellular space / extracellular region / metal ion binding
Similarity search - Function
CBS domain-containing protein, bacteria / : / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / 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 ...CBS domain-containing protein, bacteria / : / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / 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 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / MHC class I antigen / Inosine monophosphate dehydrogenase-related protein
Similarity search - Component
Biological speciesAcrocephalus arundinaceus (great reed warbler)
Vibrio sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsEltschkner, S. / Mellinger, S. / Buus, S. / Nielsen, M. / Paulsson, K.M. / Lindkvist-Petersson, K. / Westerdahl, H.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)679799European Union
CitationJournal: Front Immunol / Year: 2023
Title: The structure of songbird MHC class I reveals antigen binding that is flexible at the N-terminus and static at the C-terminus.
Authors: Eltschkner, S. / Mellinger, S. / Buus, S. / Nielsen, M. / Paulsson, K.M. / Lindkvist-Petersson, K. / Westerdahl, H.
History
DepositionApr 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
F: Inosine monophosphate dehydrogenase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0876
Polymers46,9093
Non-polymers1783
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-63 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.202, 48.780, 202.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 31630.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: exon 2-4
Source: (gene. exp.) Acrocephalus arundinaceus (great reed warbler)
Organ: liver / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O98187
#2: Protein Beta-2-microglobulin


Mass: 14205.976 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal His6-tag, TEV-cleavage site
Source: (gene. exp.) Acrocephalus arundinaceus (great reed warbler)
Gene: B2M / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A076JEK1

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Protein/peptide , 1 types, 1 molecules F

#3: Protein/peptide Inosine monophosphate dehydrogenase-related protein


Mass: 1073.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Vibrio sp. (bacteria) / References: UniProt: Q9KT74

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Non-polymers , 4 types, 170 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Hepes/MOPS, pH 7.0, 20 mM MgCl2, 40 mM CaCl2, 25 % (v/v) MPD, 25 % (w/v) PEG 1000, 25 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.15→67.38 Å / Num. obs: 22044 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.999 / Net I/σ(I): 12.1
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1759 / CC1/2: 0.848 / % possible all: 99.8

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Processing

Software
NameVersionClassification
EDNAdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMAC5.8.0258refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GJX

5gjx


Resolution: 2.15→50.58 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 13.893 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22937 1102 5 %RANDOM
Rwork0.17984 ---
obs0.18245 20877 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.065 Å2
Baniso -1Baniso -2Baniso -3
1--2.95 Å2-0 Å20 Å2
2--1.87 Å2-0 Å2
3---1.08 Å2
Refinement stepCycle: 1 / Resolution: 2.15→50.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 10 167 3328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133267
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172867
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.6564442
X-RAY DIFFRACTIONr_angle_other_deg1.3891.5816639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8965389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96121.117197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.3715506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5871528
X-RAY DIFFRACTIONr_chiral_restr0.0850.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023717
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02767
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7853.031559
X-RAY DIFFRACTIONr_mcbond_other1.7843.031558
X-RAY DIFFRACTIONr_mcangle_it2.7064.5341944
X-RAY DIFFRACTIONr_mcangle_other2.7064.5341945
X-RAY DIFFRACTIONr_scbond_it2.4693.3381708
X-RAY DIFFRACTIONr_scbond_other2.473.341709
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8434.8952498
X-RAY DIFFRACTIONr_long_range_B_refined6.47735.2633596
X-RAY DIFFRACTIONr_long_range_B_other6.47735.2793597
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 71 -
Rwork0.26 1516 -
obs--100 %
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)
15.9295-2.7298-0.99974.30260.20341.28510.04020.2439-0.2943-0.4575-0.08780.5607-0.1754-0.20580.04770.10210.0281-0.06940.0422-0.01930.0791-5.8737.8384-16.0005
25.17233.00042.1586.28622.96142.64060.0046-0.545-0.44980.2659-0.0090.66440.3092-0.17320.00440.07590.02710.0120.11410.09590.2671-7.68052.3112-7.0128
311.1520.3458-0.965111.29311.861510.92510.0877-0.42120.78191.0215-0.1250.3314-0.6874-0.29250.03730.16920.0262-0.0080.0677-0.10520.24544.243725.3326-8.6926
43.0801-1.08860.05068.49981.17082.23260.040.19520.0983-0.0235-0.1552-0.1626-0.050.06840.11520.0043-0.0084-0.00380.04830.01980.01534.785812.7984-17.6225
52.8288-2.84160.11739.1365-0.1731.63270.06880.20250.0939-0.3215-0.1575-0.3326-0.02380.1250.08870.0678-0.0282-0.00060.1375-0.01340.06837.5811.49-19.5567
64.3006-3.74310.533311.358-1.31430.1570.02850.1009-0.1671-0.0802-0.0256-0.06480.0140.0215-0.00280.12020.03530.01480.1639-0.02220.090914.85769.4235-17.4144
75.0893-1.25931.79986.3268-3.17417.9606-0.15660.25180.6058-0.0171-0.2308-0.1862-0.30860.4840.38740.0181-0.0213-0.02470.0590.0060.120216.976416.603-10.8984
812.61910.13183.06969.39212.3882.55140.2799-0.2054-0.31630.4978-0.13970.00490.29880.1036-0.14020.13920.0441-0.02860.0291-0.03260.19356.0357-3.5735-11.4416
91.1003-1.63174.01352.4596-6.027214.7847-0.01050.0133-0.0459-0.0314-0.0177-0.02930.03160.02730.02820.31370.0053-0.00630.2228-0.03910.3008-10.5706-10.0781-29.9133
101.66332.1214-2.31564.4086-0.18428.2993-0.06070.22950.089-0.26380.2996-0.0929-0.5261-0.0918-0.23890.2927-0.11560.00510.3724-0.0810.304-12.94794.7984-46.3779
111.67380.3971-1.76260.51490.10739.3255-0.00530.3578-0.1174-0.24450.1842-0.17540.16760.6714-0.17890.3526-0.0418-0.01160.4044-0.15190.3077-8.37720.5619-48.9944
129.60471.5233.56323.3127-0.62334.7853-0.11010.4339-0.59-0.03720.20540.03590.07490.5881-0.09530.27590.021-0.00480.1986-0.00740.295610.202534.8842-18.1205
1312.1046.47441.94414.93712.31983.11870.0760.09550.01340.05570.2007-0.3543-0.21360.1249-0.27680.20270.0191-0.03720.17090.03870.1396-4.877621.61-31.9119
1411.78091.82972.43257.80443.19443.5802-0.0020.3918-0.6285-0.17850.030.59920.3916-0.3899-0.0280.2176-0.0718-0.02830.21220.010.1169-23.02383.7879-37.7294
152.98374.13671.46118.42474.61516.8528-0.1271-0.04680.29010.13370.05830.0059-0.0242-0.02030.06890.07630.0492-0.06210.1255-0.00010.1324-8.283218.6805-27.3212
1613.99662.12939.98351.44521.56377.1620.0202-0.18650.21660.0915-0.09580.07650.0317-0.17910.07570.13160.00120.00820.21690.05370.1871-23.348819.045-32.2478
1711.42290.7352-1.01890.27020.02650.23010.23590.07910.111-0.2568-0.1081-0.1916-0.1358-0.2557-0.12790.34210.10760.24660.48160.09930.1793-24.870414.0228-26.8986
188.5525-0.4237-1.35394.3099-1.08741.9857-0.22310.3374-0.0944-0.03310.1165-0.0820.2313-0.13990.10660.0986-0.0198-0.02510.1206-0.04230.0519-1.999513.5277-24.8059
196.57160.99421.79122.7439-0.81613.2437-0.00930.0689-0.0411-0.3597-0.04710.25520.5077-0.19020.05640.12030.00260.01850.1723-0.00180.1064-21.357710.5338-33.2716
2010.80298.44237.48687.80556.60916.4282-0.40360.41820.6035-0.65080.2137-0.0363-0.84230.06310.18990.30590.06310.03790.18270.07520.3002-16.200623.8385-34.8447
216.60728.04693.522511.04335.87556.0333-0.33130.23590.0157-0.5830.13280.2830.06570.03650.19850.21130.0127-0.03550.23090.01510.1328-20.719312.4625-43.0777
226.82344.81981.34448.51840.97684.14310.1124-0.2075-0.48430.2013-0.1164-0.20520.2909-0.22870.0040.07680.05090.00860.1146-0.01190.09964.08048.515-7.6995
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 43
2X-RAY DIFFRACTION2A44 - 76
3X-RAY DIFFRACTION3A77 - 84
4X-RAY DIFFRACTION4A85 - 108
5X-RAY DIFFRACTION5A109 - 120
6X-RAY DIFFRACTION6A121 - 131
7X-RAY DIFFRACTION7A132 - 152
8X-RAY DIFFRACTION8A153 - 174
9X-RAY DIFFRACTION9A175 - 187
10X-RAY DIFFRACTION10A188 - 211
11X-RAY DIFFRACTION11A212 - 275
12X-RAY DIFFRACTION12B-2 - 4
13X-RAY DIFFRACTION13B5 - 13
14X-RAY DIFFRACTION14B14 - 29
15X-RAY DIFFRACTION15B30 - 39
16X-RAY DIFFRACTION16B40 - 49
17X-RAY DIFFRACTION17B50 - 56
18X-RAY DIFFRACTION18B57 - 66
19X-RAY DIFFRACTION19B67 - 81
20X-RAY DIFFRACTION20B82 - 96
21X-RAY DIFFRACTION21B97 - 104
22X-RAY DIFFRACTION22F1 - 9

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