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- PDB-4nzt: Crystal structure of the antibody-binding region of Protein M (Pr... -

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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 / Protein M, smaller domain / Protein M, C-terminal ...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 / Protein M, smaller domain / Protein M, C-terminal / 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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