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- PDB-8bqu: Molecular basis of ZP3/ZP1 heteropolymerization: crystal structur... -

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Basic information

Entry
Database: PDB / ID: 8bqu
TitleMolecular basis of ZP3/ZP1 heteropolymerization: crystal structure of a native vertebrate egg coat filament
Components
  • (Choriogenin H) x 2
  • Zona pellucida sperm-binding protein 3
KeywordsSTRUCTURAL PROTEIN / Cell adhesion / fertilization / egg-sperm interaction / gamete recognition / sperm receptor / extracellular matrix / egg coat / zona pellucida / vitelline envelope / fish chorion / glycoprotein / N-glycan / ZP module / ZP-N domain / ZP_C domain / trefoil domain / medaka / Japanese rice fish
Function / homology
Function and homology information


egg coat formation / egg coat / structural constituent of egg coat / positive regulation of acrosome reaction / binding of sperm to zona pellucida / single fertilization / extracellular region / plasma membrane
Similarity search - Function
: / P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. ...: / P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain
Similarity search - Domain/homology
Zona pellucida sperm-binding protein 4 / Zona pellucida sperm-binding protein 3
Similarity search - Component
Biological speciesOryzias latipes (Japanese medaka)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBokhove, M. / de Sanctis, D. / Yasumasu, S. / Jovine, L.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2016-03999 Sweden
Swedish Research Council2020-04936 Sweden
Knut and Alice Wallenberg Foundation2018.0042 Sweden
Citation
Journal: Cell / Year: 2024
Title: ZP2 cleavage blocks polyspermy by modulating the architecture of the egg coat.
Authors: Shunsuke Nishio / Chihiro Emori / Benjamin Wiseman / Dirk Fahrenkamp / Elisa Dioguardi / Sara Zamora-Caballero / Marcel Bokhove / Ling Han / Alena Stsiapanava / Blanca Algarra / Yonggang Lu ...Authors: Shunsuke Nishio / Chihiro Emori / Benjamin Wiseman / Dirk Fahrenkamp / Elisa Dioguardi / Sara Zamora-Caballero / Marcel Bokhove / Ling Han / Alena Stsiapanava / Blanca Algarra / Yonggang Lu / Mayo Kodani / Rachel E Bainbridge / Kayla M Komondor / Anne E Carlson / Michael Landreh / Daniele de Sanctis / Shigeki Yasumasu / Masahito Ikawa / Luca Jovine /
Abstract: Following the fertilization of an egg by a single sperm, the egg coat or zona pellucida (ZP) hardens and polyspermy is irreversibly blocked. These events are associated with the cleavage of the N- ...Following the fertilization of an egg by a single sperm, the egg coat or zona pellucida (ZP) hardens and polyspermy is irreversibly blocked. These events are associated with the cleavage of the N-terminal region (NTR) of glycoprotein ZP2, a major subunit of ZP filaments. ZP2 processing is thought to inactivate sperm binding to the ZP, but its molecular consequences and connection with ZP hardening are unknown. Biochemical and structural studies show that cleavage of ZP2 triggers its oligomerization. Moreover, the structure of a native vertebrate egg coat filament, combined with AlphaFold predictions of human ZP polymers, reveals that two protofilaments consisting of type I (ZP3) and type II (ZP1/ZP2/ZP4) components interlock into a left-handed double helix from which the NTRs of type II subunits protrude. Together, these data suggest that oligomerization of cleaved ZP2 NTRs extensively cross-links ZP filaments, rigidifying the egg coat and making it physically impenetrable to sperm.
#1: Journal: J Mol Biol / Year: 1985
Title: Mouse egg extracellular coat is a matrix of interconnected filaments possessing a structural repeat.
Authors: Greve, J.M. / Wassarman, P.M.
#2: Journal: J Biochem / Year: 1989
Title: Purification and partial characterization of high choriolytic enzyme (HCE), a component of the hatching enzyme of the teleost, Oryzias latipes.
Authors: Yasumasu, S. / Yamagami, K. / Iuchi, I.
#3: Journal: J Biochem / Year: 1989
Title: Isolation and some properties of low choriolytic enzyme (LCE), a component of the hatching enzyme of the teleost, Oryzias latipes.
Authors: Yasumasu, S. / Iuchi, I. / Yamagami, K.
#4: Journal: Dev Biol / Year: 1992
Title: Isolation of cDNAs for LCE and HCE, two constituent proteases of the hatching enzyme of Oryzias latipes, and concurrent expression of their mRNAs during development.
Authors: Yasumasu, S. / Yamada, K. / Akasaka, K. / Mitsunaga, K. / Iuchi, I. / Shimada, H. / Yamagami, K.
#5: Journal: Proc Natl Acad Sci U S A / Year: 1997
Title: Cloning of cDNA and estrogen-induced hepatic gene expression for choriogenin H, a precursor protein of the fish egg envelope (chorion).
Authors: Murata, K. / Sugiyama, H. / Yasumasu, S. / Iuchi, I. / Yasumasu, I. / Yamagami, K.
#6: Journal: Dev Biol / Year: 1995
Title: Cloning of cDNAs for the precursor protein of a low-molecular-weight subunit of the inner layer of the egg envelope (chorion) of the fish Oryzias latipes.
Authors: Murata, K. / Sasaki, T. / Yasumasu, S. / Iuchi, I. / Enami, J. / Yasumasu, I. / Yamagami, K.
#7: Journal: Dev Growth Differ / Year: 1998
Title: The third egg envelope subunit in fish: cDNA cloning and analysis, and gene expression.
Authors: Sugiyama, H. / Yasumasu, S. / Murata, K. / Iuchi, I. / Yamagami, K.
#8: Journal: J Biochem / Year: 1999
Title: Formation of mature egg envelope subunit proteins from their precursors (choriogenins) in the fish, Oryzias latipes: loss of partial C-terminal sequences of the choriogenins.
Authors: Sugiyama, H. / Murata, K. / Iuchi, I. / Nomura, K. / Yamagami, K.
#9: Journal: Nature / Year: 2008
Title: Crystal structure of the ZP-N domain of ZP3 reveals the core fold of animal egg coats.
Authors: Monne, M. / Han, L. / Schwend, T. / Burendahl, S. / Jovine, L.
#10: Journal: J Biochem / Year: 2010
Title: Mechanism of egg envelope digestion by hatching enzymes, HCE and LCE in medaka, Oryzias latipes.
Authors: Yasumasu, S. / Kawaguchi, M. / Ouchi, S. / Sano, K. / Murata, K. / Sugiyama, H. / Akema, T. / Iuchi, I.
#11: Journal: Cell / Year: 2010
Title: Insights into egg coat assembly and egg-sperm interaction from the X-ray structure of full-length ZP3.
Authors: Ling Han / Magnus Monné / Hiroki Okumura / Thomas Schwend / Amy L Cherry / David Flot / Tsukasa Matsuda / Luca Jovine /
Abstract: ZP3, a major component of the zona pellucida (ZP) matrix coating mammalian eggs, is essential for fertilization by acting as sperm receptor. By retaining a propeptide that contains a polymerization- ...ZP3, a major component of the zona pellucida (ZP) matrix coating mammalian eggs, is essential for fertilization by acting as sperm receptor. By retaining a propeptide that contains a polymerization-blocking external hydrophobic patch (EHP), we determined the crystal structure of an avian homolog of ZP3 at 2.0 Å resolution. The structure unveils the fold of a complete ZP domain module in a homodimeric arrangement required for secretion and reveals how EHP prevents premature incorporation of ZP3 into the ZP. This suggests mechanisms underlying polymerization and how local structural differences, reflected by alternative disulfide patterns, control the specificity of ZP subunit interaction. Close relative positioning of a conserved O-glycan important for sperm binding and the hypervariable, positively selected C-terminal region of ZP3 suggests a concerted role in the regulation of species-restricted gamete recognition. Alternative conformations of the area around the O-glycan indicate how sperm binding could trigger downstream events via intramolecular signaling.
#12: Journal: Curr Top Dev Biol / Year: 2018
Title: Structure of Zona Pellucida Module Proteins.
Authors: Marcel Bokhove / Luca Jovine /
Abstract: The egg coat, an extracellular matrix made up of glycoprotein filaments, plays a key role in animal fertilization by acting as a gatekeeper for sperm. Egg coat components polymerize using a common ...The egg coat, an extracellular matrix made up of glycoprotein filaments, plays a key role in animal fertilization by acting as a gatekeeper for sperm. Egg coat components polymerize using a common zona pellucida (ZP) "domain" module that consists of two related immunoglobulin-like domains, called ZP-N and ZP-C. The ZP module has also been recognized in a large number of other secreted proteins with different biological functions, whose mutations are linked to severe human diseases. During the last decade, tremendous progress has been made toward understanding the atomic architecture of the ZP module and the structural basis of its polymerization. Moreover, sperm-binding regions at the N-terminus of mollusk and mammalian egg coat subunits were found to consist of domain repeats that also adopt a ZP-N fold. This discovery revealed an unexpected link between invertebrate and vertebrate fertilization and led to the first structure of an egg coat-sperm protein recognition complex. In this review we summarize these exciting findings, discuss their functional implications, and outline future challenges that must be addressed in order to develop a comprehensive view of this family of biomedically important extracellular molecules.
#13: Journal: EMBO J / Year: 2020
Title: Cryo-EM structure of native human uromodulin, a zona pellucida module polymer.
Authors: Alena Stsiapanava / Chenrui Xu / Martina Brunati / Sara Zamora-Caballero / Céline Schaeffer / Marcel Bokhove / Ling Han / Hans Hebert / Marta Carroni / Shigeki Yasumasu / Luca Rampoldi / ...Authors: Alena Stsiapanava / Chenrui Xu / Martina Brunati / Sara Zamora-Caballero / Céline Schaeffer / Marcel Bokhove / Ling Han / Hans Hebert / Marta Carroni / Shigeki Yasumasu / Luca Rampoldi / Bin Wu / Luca Jovine /
Abstract: Assembly of extracellular filaments and matrices mediating fundamental biological processes such as morphogenesis, hearing, fertilization, and antibacterial defense is driven by a ubiquitous ...Assembly of extracellular filaments and matrices mediating fundamental biological processes such as morphogenesis, hearing, fertilization, and antibacterial defense is driven by a ubiquitous polymerization module known as zona pellucida (ZP) "domain". Despite the conservation of this element from hydra to humans, no detailed information is available on the filamentous conformation of any ZP module protein. Here, we report a cryo-electron microscopy study of uromodulin (UMOD)/Tamm-Horsfall protein, the most abundant protein in human urine and an archetypal ZP module-containing molecule, in its mature homopolymeric state. UMOD forms a one-start helix with an unprecedented 180-degree twist between subunits enfolded by interdomain linkers that have completely reorganized as a result of propeptide dissociation. Lateral interaction between filaments in the urine generates sheets exposing a checkerboard of binding sites to capture uropathogenic bacteria, and UMOD-based models of heteromeric vertebrate egg coat filaments identify a common sperm-binding region at the interface between subunits.
#14: Journal: Zoological Lett / Year: 2022
Title: Targeted deletion of liver-expressed Choriogenin L results in the production of soft eggs and infertility in medaka, Oryzias latipes.
Authors: Murata, K. / Kinoshita, M.
History
DepositionNov 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zona pellucida sperm-binding protein 3
B: Choriogenin H
C: Choriogenin H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7604
Polymers71,4843
Non-polymers1,2761
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Fragments belonging to adjacent asymmetric units pack head-to-tail to reconstitute the native heteropolymeric state of their components, generating pseudo-infinite ...Evidence: electron microscopy, Fragments belonging to adjacent asymmetric units pack head-to-tail to reconstitute the native heteropolymeric state of their components, generating pseudo-infinite filaments that run parallel to the long c axis of the crystal unit cells.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.059, 59.059, 473.919
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Zona pellucida sperm-binding protein 3


Mass: 34873.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ZP-N domain + interdomain linker + ZP-C domain / Source: (natural) Oryzias latipes (Japanese medaka) / References: UniProt: Q91184
#2: Protein Choriogenin H


Mass: 18734.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: C-terminal half of the ZP-N/ZP-C interdomain linker + ZP-C domain
Source: (natural) Oryzias latipes (Japanese medaka) / References: UniProt: P79817
#3: Protein Choriogenin H


Mass: 17876.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Trefoil domain + ZP-N domain + N-terminal half of the ZP-N/ZP-C interdomain linker
Source: (natural) Oryzias latipes (Japanese medaka) / Plasmid details: Egg vitelline envelope / References: UniProt: P79817
#4: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1276.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-1-2-3-1-4-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e4-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
Has ligand of interestY

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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: 3.46 Å3/Da / Density % sol: 64.16 % / Description: Bipyramidal prismatic
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 8
Details: 22% (w/v) PEG 3350, 0.2 M sodium/potassium phosphate, 0.1 M Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97938 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 2.419→51.147 Å / Num. obs: 14348 / % possible obs: 89.9 % / Redundancy: 4.39 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.994 / CC1/2 anomalous: 0.026 / Rmerge(I) obs: 0.1987 / Rpim(I) all: 0.1024 / Rrim(I) all: 0.2248 / AbsDiff over sigma anomalous: 0.803 / Baniso tensor eigenvalue 1: 124.6775 Å2 / Baniso tensor eigenvalue 2: 124.6775 Å2 / Baniso tensor eigenvalue 3: 0 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 3.96 Å / Aniso diffraction limit 2: 3.96 Å / Aniso diffraction limit 3: 2.257 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 6.17 / Num. measured all: 63019 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 88.6 / % possible ellipsoidal: 89.9 / % possible ellipsoidal anomalous: 88.6 / % possible spherical: 37.3 / % possible spherical anomalous: 33 / Redundancy anomalous: 2.61 / Signal type: local
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
9.658-51.1473.780.046918.05271027107167160.9980.2790.02520.05380.77199.49799.49799.42.8497
7.56-9.6584.70.08113.63337533757187180.996-0.0570.03990.09070.79610098.610098.61002.9298.6
6.543-7.564.240.15217.9304130417187180.989-0.0790.07910.17250.76699.899.299.899.299.82.699.2
5.917-6.5434.380.20096.38315731577207200.987-0.0050.10460.22760.83199.298.599.298.599.22.6298.5
5.479-5.9174.890.19636.71348734877137130.992-0.0350.09580.21960.79399.898.399.898.399.82.8898.3
5.138-5.4794.90.18336.99352635267207200.993-0.0290.09010.20520.75798.89998.89998.82.899
4.866-5.1384.820.19696.47345434547167160.993-0.0190.09770.22110.81299.199.299.199.299.12.8899.2
4.647-4.8664.730.24735.55339233927177170.9920.0750.12410.27780.83210099.410099.41002.6699.4
4.464-4.6474.320.22095.54310931097197190.9900.11490.250.79199.899.699.899.699.82.5199.6
4.303-4.4644.650.28754.95333633367177170.991-0.0320.14620.32380.8199.899.499.899.499.82.699.4
4.163-4.3034.80.34454.24344434447177170.9860.0070.17060.38640.79299.598.299.598.299.52.7798.2
4.015-4.1634.960.32744.76354935497167160.9830.0240.15860.36510.78580.281.280.281.280.22.7881.2
3.839-4.0154.640.32384.91334333437207200.976-0.0550.16410.36450.80568.171.968.158.155.82.6771.9
3.663-3.8394.560.32414.75326632667167160.976-0.0210.16690.36620.76476.97976.950.846.92.6179
3.492-3.6634.50.3624.35324032407207200.980.0020.1860.40890.83783.284.983.241.838.52.684.9
3.319-3.4924.240.31534.66302530257137130.9820.0620.16710.35880.84183.386.783.33430.42.4886.7
3.136-3.3194.090.35834.29294229427207200.963-0.0020.19230.40880.81584.285.484.226.222.92.3985.4
2.945-3.1363.930.37544.04281328137167160.970.0450.20430.430.84383.384.783.319.9172.3484.7
2.745-2.9453.650.49933.11261226127167160.8670.1010.28380.57830.83985.588.785.514.511.52.288.7
2.419-2.7453.050.61482.17219821987207200.720.0060.38890.73370.75461.97061.96.14.11.9270

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Processing

Software
NameVersionClassification
autoPROC1.0.5 20220608data processing
XDSJan 10, 2022data reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
PHENIXdev_4742refinement
STARANISO2.3.87data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble derived from PDB ID 7ZBM

7zbm
PDB Unreleased entry


Resolution: 2.7→51.147 Å / SU ML: 0.3019 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9194
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.307 646 4.69 %
Rwork0.2473 13141 -
obs0.25 13787 49.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.55 Å2
Refinement stepCycle: LAST / Resolution: 2.7→51.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4766 0 86 0 4852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324978
X-RAY DIFFRACTIONf_angle_d0.60356800
X-RAY DIFFRACTIONf_chiral_restr0.0461790
X-RAY DIFFRACTIONf_plane_restr0.006877
X-RAY DIFFRACTIONf_dihedral_angle_d11.0631803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.970.4926500.3343936X-RAY DIFFRACTION14.61
2.97-3.40.3742790.30071595X-RAY DIFFRACTION24.5
3.4-4.290.32021460.24973734X-RAY DIFFRACTION55.87
4.29-51.1470.27643710.23066876X-RAY DIFFRACTION98.79
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)
1-0.0019168707210.00600642813723-0.003540535822720.0106199164748-0.003088899631190.00457009150290.003890428141880.0118791545469-0.007038348370640.0002297912593730.001702884803030.0133077920582-0.015996918023-0.008072809352284.82178806033E-90.267197921707-0.05806951024990.1083005623940.04471782766960.02312054090590.031410660595725.5161767554-19.1597344069-5.76830899184
20.001260286963490.0117597698194-0.003698759925690.00157817185278-8.25725494654E-50.0032742923515-0.008711124573490.05700300631990.00477439059358-0.0596459981276-0.0210607365670.003560135144010.00416126361157-0.0115598217881-7.90064981524E-10-0.106426619898-0.193279432517-0.0691447016627-0.122144022768-0.0514484901039-0.10540655384230.5103314531-20.7940964223-45.3016360698
30.000440768985925-0.0003899135339550.0001245924794990.000106084797618-9.46589044384E-58.12105202252E-50.001561874248570.000985025742157-0.00234892999653-0.001916978978810.000402092910813-0.000946135439334-0.00531467631431-0.000162916802477-3.87549680502E-70.2721278445750.0103626260727-0.01398216778440.261917188694-0.01368120820980.28775488432940.1023670793-5.36900410377-49.2231777627
40.0004301300499390.001540748627960.001136456900150.000846993266259-0.0001131022520970.000382756463219-0.003557284771960.005969288260340.00605975008842-0.00302156998383-0.003758926482380.00191020724422-0.00296735593623-0.00531750230853-5.31532243085E-90.328033094816-0.0942653923056-0.09955926026270.31457147440.01773212443440.3178356825743.0735893028-3.11953579398-87.1656681534
50.001483168828290.01822088381360.002679783317210.003338172243585.76829506209E-50.00197701549898-0.0124269797073-0.0152719148199-0.0291198485969-0.00243151832562-0.008737329321150.01032676782420.0055426855610.00464801449891-5.32162204053E-90.0662952723004-0.251805451872-0.1240215573180.0590240904617-0.03136642687280.094327484547834.0729064612-20.4974291489-84.1785176739
60.01151219909510.0173572842444-0.001524998648010.007711286104910.001464258720530.003667658405890.01296371663190.00648837111953-0.007474862855580.02694982724870.0185455691929-0.054030537555-0.003292675986680.00441042987072-6.94767419448E-10-0.109566891918-0.0504356528196-0.04538876647080.206930371018-0.009357556234390.060587217626333.6043746177-21.3123163558-125.282336729
70.000316080220929-0.000335045296069-0.0002464735442526.23935195871E-50.001118140873660.00110242509524-0.00170030357988-0.00292521422593-0.00381799070348-0.00251462016990.002047865052373.82382866704E-50.00199002431852-0.001095902761633.18668976164E-60.338540606779-0.0022072061129-0.01778399492140.352897806630.006676376591760.35758890908323.4827577547-28.5804141622-156.237713862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resi 77:181)AA77 - 181
2X-RAY DIFFRACTION2(chain B and resi 398:405)BB398 - 405
3X-RAY DIFFRACTION3(chain B and resi 406:423)BB406 - 423
4X-RAY DIFFRACTION4(chain C and resi 229:269)CC229 - 269
5X-RAY DIFFRACTION5(chain C and resi 270:373)CC270 - 373
6X-RAY DIFFRACTION6(chain A and resi 207:363)AA207 - 363
7X-RAY DIFFRACTION7(chain A and resi 364:374)AA364 - 374
8X-RAY DIFFRACTION1(chain B and resi 388:397)BB388 - 397
9X-RAY DIFFRACTION2(chain B and resi 424:552)BB424 - 552
10X-RAY DIFFRACTION5(chain A and resi 194:206)AA194 - 206
11X-RAY DIFFRACTION5(chain C and resi 374:387)CC374 - 387
12X-RAY DIFFRACTION2(chain A and resi 182:193)AA182 - 193

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