[English] 日本語
Yorodumi
- PDB-9c38: Nir1 NirD domain dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9c38
TitleNir1 NirD domain dimer
ComponentsMembrane-associated phosphatidylinositol transfer protein 3
KeywordsLIPID TRANSPORT / dimerization domain
Function / homology
Function and homology information


Synthesis of PI / phosphatidylinositol transfer activity / phospholipase activity / phosphatidylinositol biosynthetic process / endomembrane system / cell projection / receptor tyrosine kinase binding / cell body / lipid binding / calcium ion binding ...Synthesis of PI / phosphatidylinositol transfer activity / phospholipase activity / phosphatidylinositol biosynthetic process / endomembrane system / cell projection / receptor tyrosine kinase binding / cell body / lipid binding / calcium ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
DDHD domain / DDHD domain / PITM 1-3, LNS2 domain / PITM 1-3, beta-sandwich domain / DDHD domain profile. / DDHD / Phosphatidylinositol transfer protein / LNS2/PITP / LNS2 / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Membrane-associated phosphatidylinositol transfer protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRahn, T.A. / Airola, M.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128666 United States
CitationJournal: To Be Published
Title: Nir1 NirD domain dimer
Authors: Rahn, T.A. / Lee, W.R. / Li, W.T. / Airola, M.V. / Liou, J.
History
DepositionMay 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Membrane-associated phosphatidylinositol transfer protein 3


Theoretical massNumber of molelcules
Total (without water)42,2671
Polymers42,2671
Non-polymers00
Water4,828268
1
A: Membrane-associated phosphatidylinositol transfer protein 3

A: Membrane-associated phosphatidylinositol transfer protein 3


Theoretical massNumber of molelcules
Total (without water)84,5342
Polymers84,5342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3650 Å2
ΔGint-30 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.403, 69.403, 150.553
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-878-

HOH

21A-888-

HOH

-
Components

#1: Protein Membrane-associated phosphatidylinositol transfer protein 3 / Phosphatidylinositol transfer protein / membrane-associated 3 / PITPnm 3 / Pyk2 N-terminal domain- ...Phosphatidylinositol transfer protein / membrane-associated 3 / PITPnm 3 / Pyk2 N-terminal domain-interacting receptor 1 / NIR-1


Mass: 42266.859 Da / Num. of mol.: 1 / Mutation: residues 287-342 and 493-531 deleted
Source method: isolated from a genetically manipulated source
Details: truncation of 974 amino acid isoform 1(Uniprot: Q9BZ71-1). This construct has residues 119-286, 343-492, 532-604.
Source: (gene. exp.) Homo sapiens (human) / Gene: PITPNM3, NIR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BZ71
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris, pH 7.5, 8.5% isoproponal, 21% glycerol, 12% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→29.87 Å / Num. obs: 27623 / % possible obs: 94.95 % / Redundancy: 22.5 % / Biso Wilson estimate: 19.5 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.2789 / Rpim(I) all: 0.06057 / Rrim(I) all: 0.2855 / Net I/σ(I): 6.28
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 23.4 % / Rmerge(I) obs: 2.671 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 2366 / CC1/2: 0.657 / CC star: 0.891 / Rpim(I) all: 0.5606 / Rrim(I) all: 2.73 / % possible all: 87.63

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→29.87 Å / SU ML: 0.184 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 19.681
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2034 1370 5.22 %
Rwork0.1717 24889 -
obs0.1734 26259 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.73 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 0 268 2688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01382501
X-RAY DIFFRACTIONf_angle_d1.0823414
X-RAY DIFFRACTIONf_chiral_restr0.0659390
X-RAY DIFFRACTIONf_plane_restr0.0158436
X-RAY DIFFRACTIONf_dihedral_angle_d5.1323340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.020.33441150.29232251X-RAY DIFFRACTION87.63
2.02-2.10.3181170.23082292X-RAY DIFFRACTION88.99
2.1-2.20.21391190.20012360X-RAY DIFFRACTION91.81
2.2-2.310.22771210.17542432X-RAY DIFFRACTION93.45
2.31-2.460.19981540.15532417X-RAY DIFFRACTION94.52
2.46-2.650.21240.15072525X-RAY DIFFRACTION96.86
2.65-2.910.18881360.15772559X-RAY DIFFRACTION97.61
2.91-3.330.1881730.15242573X-RAY DIFFRACTION98.99
3.33-4.20.16931500.14042656X-RAY DIFFRACTION99.61
4.2-29.870.19511610.17792824X-RAY DIFFRACTION99.67
Refinement TLS params.Method: refined / Origin x: 37.2283722294 Å / Origin y: 10.9721772812 Å / Origin z: 70.094406447 Å
111213212223313233
T0.0828730431129 Å2-6.18430746437E-5 Å20.00502528987136 Å2-0.133748468184 Å20.00659403174339 Å2--0.113613577569 Å2
L1.16197047515 °2-0.253314588525 °2-0.343328990428 °2-0.84550028392 °20.0619270800043 °2--1.14642712549 °2
S0.00560986368672 Å °-0.0635049672003 Å °-0.0506680098697 Å °0.00374794464078 Å °-0.0205055384477 Å °-0.0843173817145 Å °0.0907590519029 Å °0.18544416173 Å °0.0101215416569 Å °
Refinement TLS groupSelection details: all

+
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