[English] 日本語
Yorodumi
- PDB-4nzt: Crystal structure of the antibody-binding region of Protein M (Pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nzt
TitleCrystal structure of the antibody-binding region of Protein M (Protein M TD) in complex with anti-infleunza hemagglutinin antibody CR9114 Fab
Components
  • CR9114 heavy chain
  • CR9114 light chain
  • Protein M TD
KeywordsPROTEIN BINDING/IMMUNE SYSTEM / Leucine-rich repeat / broad antibody-binding / block antibody-antigen union / variable region / PROTEIN BINDING-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Pectate Lyase C-like - #180 / Translation Initiation Factor IF3 - #180 / Ribosomal Protein S8; Chain: A, domain 1 - #200 / IgG-blocking protein M / : / Protein M, large region / IgG-blocking virulence domain / Translation Initiation Factor IF3 / Pectate Lyase C-like / Ribosomal Protein S8; Chain: A, domain 1 ...Pectate Lyase C-like - #180 / Translation Initiation Factor IF3 - #180 / Ribosomal Protein S8; Chain: A, domain 1 - #200 / IgG-blocking protein M / : / Protein M, large region / IgG-blocking virulence domain / Translation Initiation Factor IF3 / Pectate Lyase C-like / Ribosomal Protein S8; Chain: A, domain 1 / 3 Solenoid / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein MG281
Similarity search - Component
Biological speciesMycoplasma genitalium (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.497 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: Science / Year: 2014
Title: A structurally distinct human mycoplasma protein that generically blocks antigen-antibody union.
Authors: Rajesh K Grover / Xueyong Zhu / Travis Nieusma / Teresa Jones / Isabel Boreo / Amanda S MacLeod / Adam Mark / Sherry Niessen / Helen J Kim / Leopold Kong / Nacyra Assad-Garcia / Keehwan Kwon ...Authors: Rajesh K Grover / Xueyong Zhu / Travis Nieusma / Teresa Jones / Isabel Boreo / Amanda S MacLeod / Adam Mark / Sherry Niessen / Helen J Kim / Leopold Kong / Nacyra Assad-Garcia / Keehwan Kwon / Marta Chesi / Vaughn V Smider / Daniel R Salomon / Diane F Jelinek / Robert A Kyle / Richard B Pyles / John I Glass / Andrew B Ward / Ian A Wilson / Richard A Lerner /
Abstract: We report the discovery of a broadly reactive antibody-binding protein (Protein M) from human mycoplasma. The crystal structure of the ectodomain of transmembrane Protein M differs from other known ...We report the discovery of a broadly reactive antibody-binding protein (Protein M) from human mycoplasma. The crystal structure of the ectodomain of transmembrane Protein M differs from other known protein structures, as does its mechanism of antibody binding. Protein M binds with high affinity to all types of human and nonhuman immunoglobulin G, predominantly through attachment to the conserved portions of the variable region of the κ and λ light chains. Protein M blocks antibody-antigen union, likely because of its large C-terminal domain extending over the antibody-combining site, blocking entry to large antigens. Similar to the other immunoglobulin-binding proteins such as Protein A, Protein M as well as its orthologs in other Mycoplasma species could become invaluable reagents in the antibody field.
History
DepositionDec 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
M: Protein M TD
H: CR9114 heavy chain
L: CR9114 light chain


Theoretical massNumber of molelcules
Total (without water)94,1903
Polymers94,1903
Non-polymers00
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-34 kcal/mol
Surface area33430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.865, 91.468, 126.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protein M TD / protein MG281


Mass: 46972.684 Da / Num. of mol.: 1 / Fragment: antibody-binding region (UNP residues 74-468)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma genitalium (bacteria) / Strain: ATCC 33530 / G-37 / NCTC 10195 / Gene: MG281 / Production host: Escherichia coli (E. coli) / References: UniProt: P47523
#2: Antibody CR9114 heavy chain


Mass: 24377.166 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#3: Antibody CR9114 light chain


Mass: 22840.172 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.29
Details: 0.1 M MES, pH 6.26, 6% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2013
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.497→50 Å / Num. obs: 27816 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rsym value: 0.13 / Net I/σ(I): 15.3
Reflection shellResolution: 2.497→2.54 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.44 / % possible all: 84.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4NZR AND 4FQH

4nzr

4fqh


Resolution: 2.497→41.727 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2458 1408 5.07 %RANDOM
Rwork0.1773 ---
obs0.1809 27757 96.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.497→41.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6210 0 0 270 6480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076364
X-RAY DIFFRACTIONf_angle_d1.1178654
X-RAY DIFFRACTIONf_dihedral_angle_d13.9882278
X-RAY DIFFRACTIONf_chiral_restr0.079956
X-RAY DIFFRACTIONf_plane_restr0.0051124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.497-2.58660.3396880.23411942X-RAY DIFFRACTION71
2.5866-2.69020.30051350.22482623X-RAY DIFFRACTION97
2.6902-2.81260.30441390.21882651X-RAY DIFFRACTION99
2.8126-2.96080.29611400.19332704X-RAY DIFFRACTION100
2.9608-3.14630.28191330.19462695X-RAY DIFFRACTION99
3.1463-3.38910.27611570.19422682X-RAY DIFFRACTION99
3.3891-3.730.26281560.17342704X-RAY DIFFRACTION99
3.73-4.26920.20751520.15382737X-RAY DIFFRACTION100
4.2692-5.3770.19911510.14372750X-RAY DIFFRACTION99
5.377-41.73330.22671570.17862861X-RAY DIFFRACTION99

+
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://pdbjlvh1.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