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- PDB-9dh2: Structure of Fab in complex with NKG2D extracellular domain -

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Basic information

Entry
Database: PDB / ID: 9dh2
TitleStructure of Fab in complex with NKG2D extracellular domain
Components
  • Fab heavy chain
  • Fab light chain
  • NKG2-D type II integral membrane protein
KeywordsIMMUNE SYSTEM / Agonist / Fab / Receptor
Function / homology
Function and homology information


negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell activation / negative regulation of GTPase activity / natural killer cell mediated cytotoxicity / stimulatory C-type lectin receptor signaling pathway / MHC class I protein binding / T cell costimulation / nitric oxide biosynthetic process ...negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell activation / negative regulation of GTPase activity / natural killer cell mediated cytotoxicity / stimulatory C-type lectin receptor signaling pathway / MHC class I protein binding / T cell costimulation / nitric oxide biosynthetic process / DAP12 interactions / positive regulation of type II interferon production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of nitric oxide biosynthetic process / DAP12 signaling / signaling receptor activity / cellular response to lipopolysaccharide / carbohydrate binding / adaptive immune response / cell differentiation / defense response to Gram-positive bacterium / external side of plasma membrane / cell surface / signal transduction / identical protein binding / membrane / plasma membrane
Similarity search - Function
NKG2-D type II integral membrane protein / Natural killer cell receptor-like, C-type lectin-like domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
NKG2-D type II integral membrane protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsFallon, D. / Huang, C.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mabs / Year: 2024
Title: Agonistic anti-NKG2D antibody structure reveals unique stoichiometry and epitope compared to natural ligands.
Authors: Fallon, D. / Huang, C.S. / Ma, J. / Morgan, C. / Zhou, Z.S.
History
DepositionSep 3, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 18, 2024Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab heavy chain
D: Fab light chain
G: Fab heavy chain
H: Fab light chain
K: Fab heavy chain
L: Fab light chain
M: NKG2-D type II integral membrane protein
P: Fab heavy chain
Q: Fab light chain
R: NKG2-D type II integral membrane protein
S: NKG2-D type II integral membrane protein
T: NKG2-D type II integral membrane protein


Theoretical massNumber of molelcules
Total (without water)251,58112
Polymers251,58112
Non-polymers00
Water00
1
A: Fab heavy chain
D: Fab light chain
K: Fab heavy chain
L: Fab light chain
M: NKG2-D type II integral membrane protein
R: NKG2-D type II integral membrane protein


Theoretical massNumber of molelcules
Total (without water)125,7916
Polymers125,7916
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Fab heavy chain
H: Fab light chain
P: Fab heavy chain
Q: Fab light chain
S: NKG2-D type II integral membrane protein
T: NKG2-D type II integral membrane protein


Theoretical massNumber of molelcules
Total (without water)125,7916
Polymers125,7916
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.062, 224.433, 136.297
Angle α, β, γ (deg.)90.00, 91.22, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
1111
1212
1313
1414
1515
1616
1717
1818

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18

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Components

#1: Antibody
Fab heavy chain


Mass: 23725.559 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody
Fab light chain


Mass: 23319.908 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Protein
NKG2-D type II integral membrane protein / Killer cell lectin-like receptor subfamily K member 1 / NK cell receptor D / NKG2-D-activating NK receptor


Mass: 15849.903 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLRK1, D12S2489E, NKG2D / Cell line (production host): Expi293 GnTI- / Production host: Homo sapiens (human) / References: UniProt: P26718
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: 2.86 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium tartrate dibasic, 20% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.98→136.64 Å / Num. obs: 56052 / % possible obs: 97.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 40.37 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.0968 / Rpim(I) all: 0.0632 / Net I/σ(I): 6.71
Reflection shellResolution: 2.98→3.03 Å / Rmerge(I) obs: 0.4005 / Num. unique obs: 8586 / CC1/2: 0.89 / Rpim(I) all: 0.2211

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→136.64 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.908 / SU B: 46.455 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.421 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24308 2758 4.9 %RANDOM
Rwork0.19708 ---
obs0.19931 53293 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.972 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å2-2.38 Å2
2--0.27 Å2-0 Å2
3----1.96 Å2
Refinement stepCycle: 1 / Resolution: 2.98→136.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17120 0 0 0 17120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01217582
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.63623922
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.19452192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.06323.947760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.699152870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9311544
X-RAY DIFFRACTIONr_chiral_restr0.1250.22318
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213260
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4422.4748810
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.523.70610988
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5582.558772
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.61332.38525154
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A60300.14
12G60300.14
21A60670.14
22K60670.14
31A61260.13
32P61260.13
41D61780.13
42H61780.13
51D61140.14
52L61140.14
61D62110.12
62Q62110.12
71G60530.14
72K60530.14
81G61030.14
82P61030.14
91H61270.13
92L61270.13
101H61290.13
102Q61290.13
111K60410.13
112P60410.13
121L61520.13
122Q61520.13
131M34880.16
132R34880.16
141M35960.15
142S35960.15
151M35810.15
152T35810.15
161R35150.15
162S35150.15
171R38030.12
172T38030.12
181S35510.15
182T35510.15
LS refinement shellResolution: 2.98→3.056 Å
RfactorNum. reflection% reflection
Rfree0.353 199 -
Rwork0.312 3873 -
obs--96.7 %
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)
11.3924-1.806-0.13213.48180.1620.20260.00550.0575-0.0351-0.01810.04450.141-0.046-0.0532-0.050.3145-0.0261-0.13750.06090.03250.095553.0938-126.9266137.592
21.9791-1.9098-0.85892.42920.97150.4249-0.2607-0.25270.03380.48770.2453-0.11240.11140.13040.01540.46660.0113-0.22960.09180.02190.124963.6294-125.5204152.733
31.40221.4699-0.35814.5981-1.06490.61470.0882-0.147-0.07250.2018-0.04080.0406-0.00550.0555-0.04740.23580.0462-0.12250.1429-0.03590.07869.963-48.069242.0258
41.6080.8341-0.40741.2559-0.32760.4025-0.02470.0095-0.0064-0.07330.04950.09030.10830.0382-0.02480.24260.0097-0.13950.02190.00190.090468.573-49.239323.6746
51.65941.3104-0.44124.3072-1.66461.79890.0371-0.1104-0.06370.35860.02590.1299-0.1068-0.1032-0.0630.24210.0363-0.1080.1061-0.02550.091244.4657-47.6713114.1466
61.55210.9994-0.26882.1796-1.19641.2184-0.10140.1143-0.0731-0.2270.17360.18740.1786-0.0951-0.07220.29830.046-0.16430.0837-0.02860.135541.804-50.022496.3142
73.00610.8166-0.04532.8588-0.77634.74740.0580.234-0.0348-0.26160.12590.33410.4505-0.5476-0.1840.40940.0065-0.16330.26260.11520.418223.3334-85.8695124.3993
82.3686-1.6565-0.10983.9308-0.29180.9570.0630.06410.0413-0.07240.03240.0927-0.0778-0.0995-0.09540.2583-0.0517-0.11580.16930.02880.073478.1637-127.59365.1287
92.6099-1.77280.67122.3559-0.55841.2835-0.1846-0.2904-0.01320.28030.25540.0552-0.1982-0.1702-0.07080.2841-0.0598-0.14240.18470.06190.113485.5672-125.787581.6178
102.8848-0.77582.21423.1577-0.32693.44160.0043-0.05950.26060.08190.04920.2603-0.1347-0.4341-0.05340.2976-0.0103-0.0540.10870.03930.262133.4264-87.5053149.0132
114.0011-1.18571.17813.1234-0.22515.027-0.1474-0.39690.29610.34750.17440.1171-0.3433-0.3464-0.0270.53160.0613-0.05440.29850.06550.358354.4195-89.561870.567
120.60050.76530.3212.5611-0.18755.8572-0.0482-0.2685-0.18560.08070.01790.0970.2859-0.44140.03030.35210.0474-0.08440.22490.10050.333847.5619-87.5244.9814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 218
2X-RAY DIFFRACTION2D1 - 211
3X-RAY DIFFRACTION3G2 - 218
4X-RAY DIFFRACTION4H1 - 211
5X-RAY DIFFRACTION5K2 - 218
6X-RAY DIFFRACTION6L1 - 211
7X-RAY DIFFRACTION7M92 - 214
8X-RAY DIFFRACTION8P2 - 218
9X-RAY DIFFRACTION9Q1 - 211
10X-RAY DIFFRACTION10R93 - 216
11X-RAY DIFFRACTION11S92 - 214
12X-RAY DIFFRACTION12T93 - 216

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