[English] 日本語
Yorodumi
- PDB-6sua: Structure of the high affinity engineered lipocalin C1B12 in comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sua
TitleStructure of the high affinity engineered lipocalin C1B12 in complex with the mouse CD98 heavy chain ectodomain
Components
  • 4F2 cell-surface antigen heavy chain
  • Neutrophil gelatinase-associated lipocalin
KeywordsPROTEIN BINDING / Lipocalin / Lcn2 / Anticalin / lipocalin-based binding protein / CD98hc / 4F2hc / amino acid transport / presentation of CD98 light chain / interaction with integrin beta subunit / single-pass type II membrane protein
Function / homology
Function and homology information


Amino acid transport across the plasma membrane / Tryptophan catabolism / apical pole of neuron / aromatic amino acid transmembrane transporter activity / amino acid transport complex / : / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / L-alanine import across plasma membrane / phenylalanine transport ...Amino acid transport across the plasma membrane / Tryptophan catabolism / apical pole of neuron / aromatic amino acid transmembrane transporter activity / amino acid transport complex / : / L-leucine import across plasma membrane / L-alanine transmembrane transporter activity / L-alanine import across plasma membrane / phenylalanine transport / L-leucine transmembrane transporter activity / L-leucine transport / neutral amino acid transport / siderophore transport / Metal sequestration by antimicrobial proteins / neutral L-amino acid transmembrane transporter activity / iron ion sequestering activity / enterobactin binding / anchoring junction / response to exogenous dsRNA / tryptophan transport / basal plasma membrane / Iron uptake and transport / specific granule lumen / double-stranded RNA binding / melanosome / positive regulation of cold-induced thermogenesis / basolateral plasma membrane / Interleukin-4 and Interleukin-13 signaling / carbohydrate metabolic process / defense response to bacterium / symbiont entry into host cell / iron ion binding / apical plasma membrane / lysosomal membrane / innate immune response / neuronal cell body / apoptotic process / synapse / Neutrophil degranulation / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Solute carrier family 3 member 2, N-terminal domain / 4F2 cell-surface antigen heavy chain / Solute carrier family 3 member 2 N-terminus / Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / Lipocalin family conserved site / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Calycin beta-barrel core domain ...Solute carrier family 3 member 2, N-terminal domain / 4F2 cell-surface antigen heavy chain / Solute carrier family 3 member 2 N-terminus / Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / Lipocalin family conserved site / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Glycosyl hydrolase, all-beta / Calycin / Lipocalin / Lipocalin signature. / Glycoside hydrolase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
4F2 cell-surface antigen heavy chain / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSchiefner, A. / Deuschle, F.-C. / Skerra, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationCollaborative Research Centre 824 project A8 Germany
CitationJournal: Protein Sci. / Year: 2020
Title: Design of a surrogate Anticalin protein directed against CD98hc for preclinical studies in mice.
Authors: Deuschle, F.C. / Schiefner, A. / Brandt, C. / Skerra, A.
History
DepositionSep 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neutrophil gelatinase-associated lipocalin
B: 4F2 cell-surface antigen heavy chain
C: Neutrophil gelatinase-associated lipocalin
D: 4F2 cell-surface antigen heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,81016
Polymers139,6584
Non-polymers1,15312
Water2,630146
1
A: Neutrophil gelatinase-associated lipocalin
B: 4F2 cell-surface antigen heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4058
Polymers69,8292
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-89 kcal/mol
Surface area25650 Å2
MethodPISA
2
C: Neutrophil gelatinase-associated lipocalin
D: 4F2 cell-surface antigen heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4058
Polymers69,8292
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-87 kcal/mol
Surface area25580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.039, 107.737, 133.872
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLYGLYAA5 - 1785 - 178
21SERSERGLYGLYCC5 - 1785 - 178
12VALVALALAALABB108 - 52616 - 434
22VALVALALAALADD108 - 52616 - 434

NCS ensembles :
ID
1
2

-
Components

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


Mass: 21462.252 Da / Num. of mol.: 2
Mutation: Q28H, A40G, I41N, Q49L, S68D, R72I, K73D, D77H, W79L, R81N, C87S, N96S, Y100T, P101L, L103S, Y106R, K125W, S127H, Y132W, K134Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Plasmid: pNGAL118 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P80188
#2: Protein 4F2 cell-surface antigen heavy chain / / 4F2hc / Solute carrier family 3 member 2


Mass: 48366.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slc3a2, Mdu1 / Plasmid: pASK-IBA5(+) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P10852
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 12 %(w/v) PEG8000, 0.2 M Li2SO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.75→34.71 Å / Num. obs: 39856 / % possible obs: 99.1 % / Redundancy: 13.198 % / Biso Wilson estimate: 42.73 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.197 / Rrim(I) all: 0.205 / Χ2: 0.944 / Net I/σ(I): 15.36 / Num. measured all: 526014 / Scaling rejects: 244
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.75-2.8511.7181.0792.4545630402938940.7691.12896.6
2.85-313.7180.8123.6869659508450780.9110.84399.9
3-3.213.990.5955.2775252538453790.9480.61899.9
3.2-3.513.7180.3469.1181496594759410.9780.3699.9
3.5-413.0230.214.9683320640463980.9920.20899.9
4-613.1890.09726.8120747926091550.9970.10198.9
6-812.2750.08827.7228183231022960.9980.09299.4
8-1013.0730.03749.631043284679810.03994.3
10-34.7112.3170.0362.171129594491710.03197.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I9Q, 6S8V

6i9q

6s8v


Resolution: 2.75→34.71 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.874 / WRfactor Rfree: 0.2251 / WRfactor Rwork: 0.1825 / FOM work R set: 0.7783 / SU B: 16.437 / SU ML: 0.314 / SU Rfree: 0.3831 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 1961 4.9 %RANDOM
Rwork0.2197 ---
obs0.2222 37895 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.8 Å2 / Biso mean: 43.758 Å2 / Biso min: 12.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å2-0 Å2-0 Å2
2---3.22 Å20 Å2
3---4.07 Å2
Refinement stepCycle: final / Resolution: 2.75→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9424 0 60 146 9630
Biso mean--65.12 28.28 -
Num. residues----1186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0139698
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178894
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.63313168
X-RAY DIFFRACTIONr_angle_other_deg1.0681.57320694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29751182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39122.932498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.552151656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8191552
X-RAY DIFFRACTIONr_chiral_restr0.0390.21220
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210734
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022006
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A54040.06
12C54040.06
21B133080.05
22D133080.05
LS refinement shellResolution: 2.75→2.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 116 -
Rwork0.342 2701 -
all-2817 -
obs--97.07 %

+
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