[English] 日本語
Yorodumi
- PDB-7fi7: Crystal structure of human MICA mutants in complex with natural k... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7fi7
TitleCrystal structure of human MICA mutants in complex with natural killer cell receptor NKG2D
Components
  • MHC class I polypeptide-related sequence A
  • NKG2-D type II integral membrane protein
KeywordsIMMUNE SYSTEM / NKG2D / MICA / thermal stability
Function / homology
Function and homology information


immune response to tumor cell / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / negative regulation of GTPase activity / gamma-delta T cell activation / positive regulation of natural killer cell mediated cytotoxicity / negative regulation of natural killer cell mediated cytotoxicity / natural killer cell activation ...immune response to tumor cell / negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / negative regulation of GTPase activity / gamma-delta T cell activation / positive regulation of natural killer cell mediated cytotoxicity / negative regulation of natural killer cell mediated cytotoxicity / natural killer cell activation / 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 / T cell mediated cytotoxicity / 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 / response to heat / carbohydrate binding / defense response to virus / adaptive immune response / killing of cells of another organism / cell differentiation / defense response to Gram-positive bacterium / defense response to bacterium / immune response / receptor ligand activity / external side of plasma membrane / DNA damage response / cell surface / signal transduction / extracellular space / identical protein binding / membrane / plasma membrane / cytoplasm
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 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 ...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 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 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
NKG2-D type II integral membrane protein / MHC class I polypeptide-related sequence A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsCai, W. / Peng, S. / Xu, T. / Tian, Y. / Li, Y. / Liu, J.
CitationJournal: to be published
Title: Crystal structure of human MICA mutants in complex with natural killer cell receptor NKG2D
Authors: Cai, W. / Peng, S. / Xu, T. / Tian, Y. / Li, Y. / Liu, J.
History
DepositionJul 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NKG2-D type II integral membrane protein
B: NKG2-D type II integral membrane protein
C: MHC class I polypeptide-related sequence A


Theoretical massNumber of molelcules
Total (without water)64,0063
Polymers64,0063
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-22 kcal/mol
Surface area25840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.254, 124.254, 184.676
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 93 - 215 / Label seq-ID: 16 - 138

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: 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: 16110.215 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLRK1, D12S2489E, NKG2D / Production host: Escherichia coli (E. coli) / References: UniProt: P26718
#2: Protein MHC class I polypeptide-related sequence A / MIC-A


Mass: 31785.590 Da / Num. of mol.: 1 / Mutation: S14M, Q109I, Q121G, L147W, Y158W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICA, PERB11.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q29983
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.82 % / Mosaicity: 0.25 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 0.1 M HEPES pH 7.5, 2.25 M Ammonium formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.78→19.835 Å / Num. obs: 18507 / % possible obs: 99.7 % / Redundancy: 25.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.026 / Rrim(I) all: 0.132 / Net I/σ(I): 23.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.78-2.9326.81.1467121326540.9070.2241.1683.6100
8.79-19.83220.0321326960210.0070.03383.291.2

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1hyr

1hyr


Resolution: 2.78→19.83 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.328 / SU ML: 0.262 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.395 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 902 4.9 %RANDOM
Rwork0.1915 ---
obs0.194 17564 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 201.11 Å2 / Biso mean: 66.986 Å2 / Biso min: 38.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å2-0 Å2
2---1.63 Å20 Å2
3---3.26 Å2
Refinement stepCycle: final / Resolution: 2.78→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4225 0 0 6 4231
Biso mean---47.69 -
Num. residues----521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134345
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173765
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.6435897
X-RAY DIFFRACTIONr_angle_other_deg1.2321.5748796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6515517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.70823.136236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.74615746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3031522
X-RAY DIFFRACTIONr_chiral_restr0.0660.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024850
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02920
Refine LS restraints NCS

Ens-ID: 1 / Number: 3536 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.16 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.78→2.851 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 61 -
Rwork0.267 1268 -
all-1329 -
obs--99.92 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more