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- PDB-7nzf: Crystal structure of HLA-DR4 in complex with a mutated human coll... -

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Basic information

Entry
Database: PDB / ID: 7nzf
TitleCrystal structure of HLA-DR4 in complex with a mutated human collagen type II peptide
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DR beta chain
  • mutant human collagen type II,259-273
KeywordsIMMUNE SYSTEM / Complex / MHCII
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGe, C. / Dobritzsch, D. / Holmdahl, R.
Funding support Sweden, 3items
OrganizationGrant numberCountry
The Swedish Foundation for Strategic Research Sweden
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Ann Rheum Dis / Year: 2022
Title: Key interactions in the trimolecular complex consisting of the rheumatoid arthritis-associated DRB1*04:01 molecule, the major glycosylated collagen II peptide and the T-cell receptor.
Authors: Ge, C. / Weisse, S. / Xu, B. / Dobritzsch, D. / Viljanen, J. / Kihlberg, J. / Do, N.N. / Schneider, N. / Lanig, H. / Holmdahl, R. / Burkhardt, H.
History
DepositionMar 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2024Group: Data collection / Structure summary / Category: audit_author / chem_comp_atom / chem_comp_bond / Item: _audit_author.name
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: HLA class II histocompatibility antigen, DR alpha chain
BBB: HLA class II histocompatibility antigen, DR beta chain
CCC: mutant human collagen type II,259-273
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9565
Polymers44,5143
Non-polymers4422
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-30 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.441, 71.441, 138.049
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein HLA class II histocompatibility antigen, DR alpha chain


Mass: 20893.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Protein HLA class II histocompatibility antigen, DR beta chain


Mass: 22432.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein/peptide mutant human collagen type II,259-273


Mass: 1187.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 290 K / Method: evaporation / Details: 0.1 M MIB buffer pH 4.0, 25 % (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91842 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91842 Å / Relative weight: 1
ReflectionResolution: 1.9→46.07 Å / Num. obs: 32456 / % possible obs: 99 % / Redundancy: 11.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.039 / Rrim(I) all: 0.095 / Net I/σ(I): 17.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.11-46.078.20.044232650.9970.0210.049
1.9-1.9411.50.83429090.8530.370.913

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J8H

1j8h


Resolution: 1.9→36.951 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.895 / SU ML: 0.132 / Cross valid method: FREE R-VALUE / ESU R: 0.182 / ESU R Free: 0.167
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2667 1564 4.83 %
Rwork0.2214 30818 -
all0.224 --
obs-32382 98.44 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.725 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å2-0 Å2
3----0.456 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 28 171 3221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133139
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172826
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.6674274
X-RAY DIFFRACTIONr_angle_other_deg1.2931.5886507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2255365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87822.053190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72315487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4931523
X-RAY DIFFRACTIONr_chiral_restr0.0780.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023549
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02769
X-RAY DIFFRACTIONr_nbd_refined0.220.2521
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.22713
X-RAY DIFFRACTIONr_nbtor_refined0.170.21468
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21600
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2148
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.217
X-RAY DIFFRACTIONr_nbd_other0.1830.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.29
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0450.21
X-RAY DIFFRACTIONr_mcbond_it0.9481.7631475
X-RAY DIFFRACTIONr_mcbond_other0.9471.7621474
X-RAY DIFFRACTIONr_mcangle_it1.5252.6351835
X-RAY DIFFRACTIONr_mcangle_other1.5252.6371836
X-RAY DIFFRACTIONr_scbond_it1.1581.9061664
X-RAY DIFFRACTIONr_scbond_other1.1571.9071665
X-RAY DIFFRACTIONr_scangle_it1.8432.8052438
X-RAY DIFFRACTIONr_scangle_other1.8432.8062439
X-RAY DIFFRACTIONr_lrange_it4.55820.6393337
X-RAY DIFFRACTIONr_lrange_other4.50320.3843312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.3641100.2672220X-RAY DIFFRACTION97.4895
1.949-2.0030.2951180.2482159X-RAY DIFFRACTION97.7673
2.003-2.0610.2751230.2442104X-RAY DIFFRACTION97.9762
2.061-2.1240.2631200.2312036X-RAY DIFFRACTION98.0446
2.124-2.1940.227780.2192014X-RAY DIFFRACTION98.0778
2.194-2.2710.242990.2111935X-RAY DIFFRACTION98.4511
2.271-2.3560.356860.2261894X-RAY DIFFRACTION98.3607
2.356-2.4520.302770.2331836X-RAY DIFFRACTION98.3548
2.452-2.5610.282930.2161729X-RAY DIFFRACTION98.5931
2.561-2.6860.271810.2151685X-RAY DIFFRACTION98.7696
2.686-2.8310.293630.2181608X-RAY DIFFRACTION98.352
2.831-3.0020.273870.2231502X-RAY DIFFRACTION98.757
3.002-3.2090.286800.2351418X-RAY DIFFRACTION98.8127
3.209-3.4650.263570.2151335X-RAY DIFFRACTION99.1453
3.465-3.7950.245760.2211249X-RAY DIFFRACTION99.1025
3.795-4.2410.271660.1991109X-RAY DIFFRACTION98.9057
4.241-4.8930.182560.1731002X-RAY DIFFRACTION99.3427
4.893-5.9830.282530.212868X-RAY DIFFRACTION99.46
5.983-8.4220.333170.275698X-RAY DIFFRACTION99.7211
8.422-36.9510.253240.253417X-RAY DIFFRACTION98
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)
11.0456-0.8191-0.18014.21510.04271.5953-0.0278-0.03480.09030.00830.09050.1306-0.1768-0.0853-0.06270.0587-0.0273-0.00230.06450.00170.022320.0395-10.0129-12.6778
21.0649-0.9234-0.79793.12331.88532.83930.11330.19130.1826-0.4371-0.03550.0355-0.7374-0.1357-0.07780.20520.00230.00210.12890.05030.048821.1596-5.8716-28.562
312.4039-2.3183-4.51221.60740.76043.8740.070.08310.9171-0.08920.0285-0.0469-0.1112-0.3352-0.09850.3091-0.0173-0.00040.1361-0.01770.221217.671613.1127-15.4013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1 - 180
2X-RAY DIFFRACTION1ALLAaA181
3X-RAY DIFFRACTION2ALLBBB2 - 190
4X-RAY DIFFRACTION3ALLCCC2 - 14

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