[English] 日本語
Yorodumi
- PDB-9f1i: Crystal structure of a first-in-class antibody for alpha-1,6-fuco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9f1i
TitleCrystal structure of a first-in-class antibody for alpha-1,6-fucosylated prostate-specific antigen, target bound
Components
  • Heavy chain rabbit fab
  • Light chain rabbit fab
  • Prostate specific antigen
KeywordsIMMUNE SYSTEM / antibody / fab / prostate-specific antigen / PSA / fucosylation / diagnostic assay
Function / homology
Function and homology information


regulation of systemic arterial blood pressure / zymogen activation / secretory granule / serine-type endopeptidase activity
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
2-[2-(2-azanylethoxy)ethoxy]ethanoic acid / Prostate specific antigen
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsHalldorsson, S.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: Sci Rep / Year: 2024
Title: Development of a first-in-class antibody and a specific assay for alpha-1,6-fucosylated prostate-specific antigen.
Authors: Halldorsson, S. / Hillringhaus, L. / Hojer, C. / Muranyi, A. / Schraeml, M. / Lange, M.S. / Tabares, G.
History
DepositionApr 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Heavy chain rabbit fab
I: Heavy chain rabbit fab
L: Light chain rabbit fab
M: Light chain rabbit fab
P: Prostate specific antigen
Q: Prostate specific antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,04616
Polymers95,6136
Non-polymers1,43310
Water14,322795
1
H: Heavy chain rabbit fab
L: Light chain rabbit fab
P: Prostate specific antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5859
Polymers47,8063
Non-polymers7796
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-12 kcal/mol
Surface area18840 Å2
MethodPISA
2
I: Heavy chain rabbit fab
M: Light chain rabbit fab
Q: Prostate specific antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4617
Polymers47,8063
Non-polymers6554
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-24 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.310, 87.395, 150.427
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Antibody , 2 types, 4 molecules HILM

#1: Antibody Heavy chain rabbit fab


Mass: 23734.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: pUC18 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Light chain rabbit fab


Mass: 22957.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Plasmid: pUC18 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

-
Protein/peptide / Sugars , 2 types, 4 molecules PQ

#3: Protein/peptide Prostate specific antigen


Mass: 1114.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8NCW4
#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

-
Non-polymers , 3 types, 803 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PFX / 2-[2-(2-azanylethoxy)ethoxy]ethanoic acid


Type: peptide-like / Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 795 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris-HCl pH 8.5, 6.25% v/v PEG 3350, 6.25% v/v PEG 4000, 6.25% v/v PEG 2000 and 6.25% v/v PEG 5000 MME

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→52.24 Å / Num. obs: 155757 / % possible obs: 95.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 27.86 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.054 / Net I/σ(I): 15.7
Reflection shellResolution: 1.38→1.49 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7791 / CC1/2: 0.633 / Rrim(I) all: 1.169 / % possible all: 65.4

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207+SVNrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→41.2 Å / SU ML: 0.1442 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4729
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1865 7799 5.01 %
Rwork0.1547 147840 -
obs0.1564 155639 79.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.82 Å2
Refinement stepCycle: LAST / Resolution: 1.38→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6672 0 24 795 7491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00516862
X-RAY DIFFRACTIONf_angle_d0.76659377
X-RAY DIFFRACTIONf_chiral_restr0.07571121
X-RAY DIFFRACTIONf_plane_restr0.00511182
X-RAY DIFFRACTIONf_dihedral_angle_d12.36072425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.390.382160.2313285X-RAY DIFFRACTION4.67
1.39-1.410.2181340.2139513X-RAY DIFFRACTION8.47
1.41-1.430.2616390.2146739X-RAY DIFFRACTION12.12
1.43-1.450.3049480.21961021X-RAY DIFFRACTION16.47
1.45-1.470.2445660.20981599X-RAY DIFFRACTION25.95
1.47-1.490.26231410.20922917X-RAY DIFFRACTION47.05
1.49-1.510.28671700.19273772X-RAY DIFFRACTION60.5
1.51-1.530.29462130.19523992X-RAY DIFFRACTION65.12
1.53-1.550.25252230.19164316X-RAY DIFFRACTION70.12
1.55-1.580.22582820.18284760X-RAY DIFFRACTION77.77
1.58-1.610.24042840.18695580X-RAY DIFFRACTION90.54
1.61-1.640.20983100.1876085X-RAY DIFFRACTION98.89
1.64-1.670.22563070.17036205X-RAY DIFFRACTION100
1.67-1.70.21283280.16866165X-RAY DIFFRACTION99.98
1.7-1.740.23873610.17256131X-RAY DIFFRACTION99.97
1.74-1.780.24343150.16816215X-RAY DIFFRACTION99.97
1.78-1.820.21273190.15346158X-RAY DIFFRACTION99.95
1.82-1.870.20283190.1466173X-RAY DIFFRACTION99.97
1.87-1.930.19023140.14446214X-RAY DIFFRACTION99.94
1.93-1.990.19673150.14686231X-RAY DIFFRACTION99.95
1.99-2.060.16513280.14346201X-RAY DIFFRACTION99.95
2.06-2.140.20323230.14756204X-RAY DIFFRACTION99.94
2.14-2.240.19013330.14696189X-RAY DIFFRACTION100
2.24-2.360.19163510.14966221X-RAY DIFFRACTION100
2.36-2.510.19033480.16366193X-RAY DIFFRACTION99.95
2.51-2.70.19723500.16496248X-RAY DIFFRACTION99.98
2.7-2.970.19733170.17256263X-RAY DIFFRACTION99.97
2.97-3.40.16993340.16396320X-RAY DIFFRACTION99.92
3.4-4.280.16573600.14426342X-RAY DIFFRACTION99.9
4.28-41.20.15323510.13316588X-RAY DIFFRACTION99.86

+
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