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- PDB-9ges: Crystal structure of HEI10 -

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Basic information

Entry
Database: PDB / ID: 9ges
TitleCrystal structure of HEI10
ComponentsE3 ubiquitin-protein ligase CCNB1IP1
KeywordsRECOMBINATION / Meiosis / E3 ligase / synaptonemal complex
Function / homology
Function and homology information


chiasma assembly / synaptonemal complex / blastocyst formation / reciprocal meiotic recombination / spermatid development / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / protein ubiquitination / zinc ion binding / identical protein binding
Similarity search - Function
E3 ubiquitin-protein ligase CCNB1IP1 / zinc-RING finger domain / Zinc finger, RING-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase CCNB1IP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsMilburn, A.E. / Espejo-Serrano, C. / Dunce, J.M. / Davies, O.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust219413/Z/19/Z United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of HEI10
Authors: Milburn, A.E. / Espejo-Serrano, C. / Dunce, J.M. / Davies, O.R.
History
DepositionAug 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase CCNB1IP1
B: E3 ubiquitin-protein ligase CCNB1IP1
C: E3 ubiquitin-protein ligase CCNB1IP1
D: E3 ubiquitin-protein ligase CCNB1IP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,90012
Polymers91,3774
Non-polymers5238
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.198, 73.857, 124.032
Angle α, β, γ (deg.)90.000, 99.276, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein
E3 ubiquitin-protein ligase CCNB1IP1 / Cyclin-B1-interacting protein 1 / Human enhancer of invasion 10 / RING-type E3 ubiquitin transferase CCNB1IP1


Mass: 22844.213 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCNB1IP1, C14orf18, HEI10 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NPC3, RING-type E3 ubiquitin transferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 2.9 Å3/Da / Density % sol: 57.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES sodium salt pH 7.5 30% (w/v) MPD; 5% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.27806 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27806 Å / Relative weight: 1
ReflectionResolution: 2.43→63.238 Å / Num. obs: 11283 / % possible obs: 31.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 42.69 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.051 / Net I/σ(I): 9.4
Reflection shellResolution: 2.43→2.781 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.201 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 565 / Rpim(I) all: 0.479 / % possible all: 4.7

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→43.46 Å / SU ML: 0.3041 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.1128
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2894 588 5.23 %
Rwork0.25 10660 -
obs0.2521 11248 31.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.51 Å2
Refinement stepCycle: LAST / Resolution: 2.43→43.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5794 0 8 0 5802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00195898
X-RAY DIFFRACTIONf_angle_d0.45637910
X-RAY DIFFRACTIONf_chiral_restr0.035852
X-RAY DIFFRACTIONf_plane_restr0.00341000
X-RAY DIFFRACTIONf_dihedral_angle_d10.21572284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.650.3421140.3864294X-RAY DIFFRACTION3.74
2.69-3.060.4009540.35631096X-RAY DIFFRACTION13.36
3.06-3.860.30071510.29372659X-RAY DIFFRACTION31.33
3.86-43.460.28053690.23076611X-RAY DIFFRACTION76.51
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)
10.841770062364-0.3109070678010.07414695288051.382798704480.7232813820620.4506927336530.1123637016370.4701137349890.22657355079-0.4594433045530.220826810175-0.36457647984-0.2772484540570.276308758969-0.1083555259730.2144116226520.0920216897979-0.0143627034350.579335020777-0.04281918329790.16022024835215.6183757218-1.582523876378.81915834566
20.9119978108210.0509033266896-0.03965646010930.03822699959520.1770298332160.8413911739460.05657482829370.1865767395880.178160153166-0.07559945269790.0779052093014-0.00638370409899-0.1179369809130.05996705023010.0137084062048-0.0521312559457-0.1212448091050.001078648063780.381856283290.1108162640510.21384437883916.7988528947-0.42803269968323.7436468602
30.2207408584840.1640501917460.182996104001-0.01751540606280.209632849970.202408689422-0.2159969224790.099912196763-0.056315077139-0.7301768254140.24250666894-0.03971633186080.0699330087087-0.0197915553473-0.0381202965350.541194413248-0.204450958968-0.1621886965610.348511371414-0.0621498284140.0824293645521-18.7356162556-7.67708548666-31.9483503532
41.36070727893-0.0825497416705-0.3176423033581.082158344360.8124849365561.46612344467-0.0215686732229-0.210165240148-0.01099114022610.02028120927880.0969508037198-0.442638836931-0.04900615304690.27128228609-0.02283589781810.0879954030727-0.04682431986310.0269294453970.4476030014470.08945679271460.13303613771225.1619853318-2.4260308197944.955338231
50.1511466206060.034127034455-0.005036655963-0.03983067511990.115165604573-0.008192048467410.0716370985087-0.016883524540.1985774187480.499556254185-0.124169629731-0.17705820775-0.026814476762-0.04064149397910.100523398682-0.04174405299810.144379911269-0.05384500014090.30031447263-0.1566491277950.014068494835116.71235481328.3668698228989.6957015495
60.166729448660.04899680937740.2122487950260.5815899631290.1306699212251.02496004855-0.0996767022235-0.1941191321540.1670839625530.390341304706-0.0337148357070.176114617069-0.349774609556-0.28218992679-0.134093621450.09522523858470.09405617492290.1148592533290.20966462626-0.313114189205-0.161293129027-12.57975029215.9155849503948.9254934468
70.1263462211910.05175222268550.523354703311-0.1464745031430.1666548158411.6918222951-0.165213743383-0.09865371092960.09011951237830.254285748218-0.1210399783930.0129075562737-0.2948350424310.11744019721-0.009351219608260.649663787858-0.0864755194435-0.3991212414050.248065683481-0.146290770018-0.098614436680818.062981405113.924062386997.624528461
81.19089867232-0.39901868454-0.2849808582580.778125606964-0.7507115256971.215121484070.03167865989440.185223319981-0.0571324270054-0.2063873446580.05208610118940.08894162372640.0769927840786-0.08722019196320.2355465143330.215835377644-0.088721157773-0.1379083361130.262808156397-0.165028871748-0.109559177715-18.3626268269-4.187941874218.494732642
92.992074983470.794650784916-1.978588785922.627191688861.517674035954.90090738979-0.217972041931-0.196541171694-0.235164320441-0.080636475661-0.0519823735661-0.1450296975530.3594489096310.2628622310020.151970885350.468443664950.1341918820550.1890829000910.641265016573-0.2405816728340.361148106301-27.4807821434-5.3525788292321.9932465286
100.190779089096-0.0701072422950.1227941136340.2175794610050.142758181390.474947602351-0.0347752045540.0355213474138-0.130616961952-0.06254852681230.02872185937520.1368461810930.0928265219565-0.193764573379-0.0173392032474-0.186370377429-0.1219817104080.003487905582320.136044386288-0.1104954023390.0448453323491-17.6921528841-3.8517903197130.8259245067
110.0598353056401-0.04907673754430.414682697684-0.198052431808-0.3182041132161.050193739320.2204027506340.04693848755910.0499946370724-0.43083174178-0.14792513370.2623823804960.2032624369760.05531740448950.07541889826970.497209097956-0.0533401776138-0.08720491053860.1596980825670.133809921418-0.0788071432567-17.8065811081-12.8232375121-31.6874605834
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 50 )AA8 - 501 - 43
22chain 'A' and (resid 51 through 81 )AA51 - 8144 - 74
33chain 'A' and (resid 82 through 184 )AA82 - 18475 - 177
44chain 'B' and (resid 8 through 65 )BB8 - 651 - 58
55chain 'B' and (resid 66 through 184 )BB66 - 18459 - 177
66chain 'C' and (resid 7 through 81 )CC7 - 811 - 75
77chain 'C' and (resid 82 through 185 )CC82 - 18576 - 179
88chain 'D' and (resid 7 through 33 )DD7 - 331 - 27
99chain 'D' and (resid 34 through 42 )DD34 - 4228 - 36
1010chain 'D' and (resid 43 through 81 )DD43 - 8137 - 75
1111chain 'D' and (resid 82 through 185 )DD82 - 18576 - 179

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