[English] 日本語
Yorodumi
- PDB-5n48: Structure of Anticalin N9B in complex with extra-domain B of huma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5n48
TitleStructure of Anticalin N9B in complex with extra-domain B of human oncofetal fibronectin
Components
  • Fibronectin
  • Neutrophil gelatinase-associated lipocalin
KeywordsPROTEIN BINDING / LIPOCALIN / ANTICALIN / LIPOCALIN-BASED BINDING PROTEIN / HUMAN FIBRONECTIN / ONCOFETAL SPLICE VARIANT / FN TYPE III DOMAIN / EXTRA-DOMAIN B / EIIIB / ED-B / EXTRACELLULAR MATRIX
Function / homology
Function and homology information


positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of monocyte activation / negative regulation of hippocampal neuron apoptotic process / negative regulation of transforming growth factor beta production / positive regulation of cell projection organization / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Metal sequestration by antimicrobial proteins ...positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of monocyte activation / negative regulation of hippocampal neuron apoptotic process / negative regulation of transforming growth factor beta production / positive regulation of cell projection organization / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Metal sequestration by antimicrobial proteins / siderophore transport / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / neural crest cell migration involved in autonomic nervous system development / response to kainic acid / response to mycotoxin / response to blue light / fibrinogen complex / cellular response to increased oxygen levels / peptide cross-linking / response to fructose / integrin activation / cellular response to X-ray / ALK mutants bind TKIs / short-term memory / cell-substrate junction assembly / cellular response to interleukin-6 / iron ion sequestering activity / enterobactin binding / proteoglycan binding / extracellular matrix structural constituent / response to herbicide / MET activates PTK2 signaling / Molecules associated with elastic fibres / peptidase activator activity / biological process involved in interaction with symbiont / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / response to iron(II) ion / response to muscle activity / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of reactive oxygen species biosynthetic process / endodermal cell differentiation / regulation of protein phosphorylation / GRB2:SOS provides linkage to MAPK signaling for Integrins / basement membrane / Non-integrin membrane-ECM interactions / cellular response to interleukin-1 / ECM proteoglycans / long-term memory / Integrin cell surface interactions / endothelial cell migration / regulation of ERK1 and ERK2 cascade / positive regulation of axon extension / cellular response to nutrient levels / collagen binding / Degradation of the extracellular matrix / extrinsic apoptotic signaling pathway in absence of ligand / Integrin signaling / extracellular matrix / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / platelet alpha granule lumen / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / wound healing / Iron uptake and transport / Signaling by high-kinase activity BRAF mutants / cellular response to nerve growth factor stimulus / MAP2K and MAPK activation / response to wounding / response to virus / specific granule lumen / integrin binding / cellular response to hydrogen peroxide / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of fibroblast proliferation / cellular response to amyloid-beta / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cellular response to tumor necrosis factor / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / Platelet degranulation / nervous system development / GPER1 signaling / regulation of cell shape / heparin binding / : / positive regulation of cold-induced thermogenesis / heart development / cellular response to lipopolysaccharide / protease binding / angiogenesis
Similarity search - Function
Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain ...Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Lipocalin / Lipocalin family conserved site / Kringle-like fold / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Fibronectin type III domain / EGF-like domain signature 1. / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Lipocalin / Fibronectin type III / Fibronectin type III superfamily / Lipocalin signature. / Immunoglobulin-like fold / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibronectin / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchiefner, A. / Skerra, A.
CitationJournal: Structure / Year: 2018
Title: Anticalins Reveal High Plasticity in the Mode of Complex Formation with a Common Tumor Antigen.
Authors: Schiefner, A. / Gebauer, M. / Richter, A. / Skerra, A.
History
DepositionFeb 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neutrophil gelatinase-associated lipocalin
B: Fibronectin
C: Neutrophil gelatinase-associated lipocalin
D: Fibronectin


Theoretical massNumber of molelcules
Total (without water)65,9884
Polymers65,9884
Non-polymers00
Water5,332296
1
A: Neutrophil gelatinase-associated lipocalin
B: Fibronectin


Theoretical massNumber of molelcules
Total (without water)32,9942
Polymers32,9942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-7 kcal/mol
Surface area13330 Å2
MethodPISA
2
C: Neutrophil gelatinase-associated lipocalin
D: Fibronectin


Theoretical massNumber of molelcules
Total (without water)32,9942
Polymers32,9942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-6 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.456, 67.801, 76.806
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Neutrophil gelatinase-associated lipocalin / NGAL / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / ...NGAL / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / Siderocalin LCN2 / p25


Mass: 21659.764 Da / Num. of mol.: 2
Mutation: Q28H, L36R, A40M, I41R, Q49A, Y52V, S68K, L70M, R72Q, K73R, D77K, W79M, R81N, C87S, N96A, Y100P, L103P, Y106T, K125H, S127F, K134H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Plasmid: pNGAL98-N9B / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P80188
#2: Protein Fibronectin / FN / Cold-insoluble globulin / CIG


Mass: 11334.474 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Plasmid: pASK35(+)-EDB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P02751
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.07 Å3/Da / Density % sol: 40.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 29 % (w/v) PEG4000, 0.1 M Na-malonate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91741 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2011
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.51
11h,-k,-l20.49
ReflectionResolution: 1.6→28.47 Å / Num. obs: 70827 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.18 % / Biso Wilson estimate: 25.453 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.065 / Χ2: 0.978 / Net I/σ(I): 14.85 / Num. measured all: 296035 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.74.1720.4233.33117140.8790.48599.8
1.7-1.84.190.275.0692600.9460.3199.8
1.8-24.1930.149.17134480.9850.1699.6
2-2.54.1820.07317.27177010.9930.08399.7
2.5-34.1730.0524.6678020.9960.05799.7
3-44.1710.04130.6462760.9970.04799.6
4-64.1820.03433.0332390.9980.03999.8
6-84.1510.03532.527940.9980.0499.6
8-104.1170.02832.782910.9980.03399.3
10-28.473.8940.03231.993020.9980.03793.2

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GH7

4gh7


Resolution: 1.6→28.47 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.449 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.019
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 3545 5 %RANDOM
Rwork0.1688 ---
obs0.1707 67277 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 54.83 Å2 / Biso mean: 22.795 Å2 / Biso min: 11.09 Å2
Baniso -1Baniso -2Baniso -3
1--10.75 Å2-0 Å21.05 Å2
2--27.05 Å20 Å2
3----16.31 Å2
Refinement stepCycle: final / Resolution: 1.6→28.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4217 0 0 296 4513
Biso mean---30.59 -
Num. residues----534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194321
X-RAY DIFFRACTIONr_bond_other_d0.0020.024097
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.9585873
X-RAY DIFFRACTIONr_angle_other_deg1.13639459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5085530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34324.421190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06315721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6421520
X-RAY DIFFRACTIONr_chiral_restr0.1170.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214828
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02972
LS refinement shellResolution: 1.598→1.64 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 240 -
Rwork0.213 4769 -
all-5009 -
obs--96.25 %
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)
10.4069-0.01160.15810.0953-0.18860.42890.02080.0051-0.0092-0.00150.00480.01870.0175-0.0039-0.02560.16420.00680.00140.0022-0.00810.145553.58294.541837.1738
20.8966-0.0423-0.21220.3445-0.71381.58760.0917-0.09290.0243-0.0494-0.06350.02160.06160.1662-0.02820.1405-0.0150.01360.0422-0.01160.112370.01741.489454.6294
30.34440.0142-0.18510.04030.16410.99030.01590.01920.01020.01040.0076-0.0187-0.0027-0.0309-0.02360.14610.00850.0180.02590.00140.121141.09932.0944-1.3041
40.777-0.06360.04740.25820.61691.55040.11770.0049-0.0029-0.0045-0.0731-0.03190.0121-0.2089-0.04460.1299-0.00720.01850.0824-0.00150.088624.55015.423516.3733
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 177
2X-RAY DIFFRACTION2B1266 - 1357
3X-RAY DIFFRACTION3C4 - 177
4X-RAY DIFFRACTION4D1265 - 1357

+
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