5JKE

Crystal structure of human IZUMO1-JUNO complex (crystal form 3)

> Summary

Summary for 5JKE

Related5JKD 5JKC 5JKB 5JKA 5JK9
DescriptorIzumo sperm-egg fusion protein 1, Sperm-egg fusion protein Juno, N-ACETYL-D-GLUCOSAMINE, ... (6 entities in total)
Functional Keywordsfertilization, izumo1, juno, cell adhesion
Biological sourceHomo sapiens (Human)
Cellular locationMembrane ; Single-pass type I membrane protein  Q8IYV9
Cell membrane ; Lipid-anchor, GPI-anchor  A6ND01
Total number of polymer chains4
Total molecular weight108332.2
Authors
Ohto, U.,Ishida, H.,Shimizu, T. (deposition date: 2016-04-26, release date: 2016-06-22, Last modification date: 2016-06-29)
Primary citation
Ohto, U.,Ishida, H.,Krayukhina, E.,Uchiyama, S.,Inoue, N.,Shimizu, T.
Structure of IZUMO1-JUNO reveals sperm-oocyte recognition during mammalian fertilization
Nature, 534:566-569, 2016
PubMed: 27309808 (PDB entries with the same primary citation)
DOI: 10.1038/nature18596
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.86 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.24450.2%3.7%2.4%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5jke
no rotation
Molmil generated image of 5jke
rotated about x axis by 90°
Molmil generated image of 5jke
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 5jke
no rotation
Molmil generated image of 5jke
rotated about x axis by 90°
Molmil generated image of 5jke
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (5jke.pdb1.gz [151.55 KB])
Coordinate files for Biological unit (5jke.pdb2.gz [151.85 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, CIzumo sperm-egg fusion protein 1polymer24628163.32
UniProt (Q8IYV9)
Pfam (PF16706)
Homo sapiens (Human)@PDBjOocyte binding/fusion factor,OBF,Sperm-specific protein izumo
B, DSperm-egg fusion protein Junopolymer22125428.82
UniProt (A6ND01)
Pfam (PF03024)
Homo sapiens (Human)@PDBjFolate receptor 4,Folate receptor delta,FR-delta,IZUMO1 receptor protein JUNO
N-ACETYL-D-GLUCOSAMINEnon-polymer221.24
SULFATE IONnon-polymer96.12
CHLORIDE IONnon-polymer35.52
waterwater18.04

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight107184.3
Non-Polymers*Number of molecules8
Total molecular weight1147.9
All*Total molecular weight108332.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.86 Å)

Cell axes64.182141.776144.861
Cell angles90.0090.0090.00
SpacegroupP 2 21 21
Resolution limits48.30 - 2.86
the highest resolution shell value2.934 - 2.860
R-factor0.20429
R-work0.20265
the highest resolution shell value0.339
R-free0.23817
the highest resolution shell value0.356
RMSD bond length0.011
RMSD bond angle1.592

Data Collection Statistics

Resolution limits48.30 - 2.86
the highest resolution shell value -
Number of reflections31399
Completeness100.0
Redundancy13.2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP293

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0002080cellular_componentacrosomal membrane
A0016021cellular_componentintegral component of membrane
A0005886cellular_componentplasma membrane
A0086080molecular_functionprotein binding involved in heterotypic cell-cell adhesion
A0042803molecular_functionprotein homodimerization activity
A0005102molecular_functionreceptor binding
A0007155biological_processcell adhesion
A0007342biological_processfusion of sperm to egg plasma membrane involved in single fertilization
A0034113biological_processheterotypic cell-cell adhesion
A0007338biological_processsingle fertilization
A0035036biological_processsperm-egg recognition
C0002080cellular_componentacrosomal membrane
C0016021cellular_componentintegral component of membrane
C0005886cellular_componentplasma membrane
C0086080molecular_functionprotein binding involved in heterotypic cell-cell adhesion
C0042803molecular_functionprotein homodimerization activity
C0005102molecular_functionreceptor binding
C0007155biological_processcell adhesion
C0007342biological_processfusion of sperm to egg plasma membrane involved in single fertilization
C0034113biological_processheterotypic cell-cell adhesion
C0007338biological_processsingle fertilization
C0035036biological_processsperm-egg recognition
B0031225cellular_componentanchored component of membrane
B0005576cellular_componentextracellular region
B0005886cellular_componentplasma membrane
B0004872molecular_functionreceptor activity
B0006501biological_processC-terminal protein lipidation
B0007155biological_processcell adhesion
B0007342biological_processfusion of sperm to egg plasma membrane involved in single fertilization
B0007338biological_processsingle fertilization
B0035036biological_processsperm-egg recognition
D0031225cellular_componentanchored component of membrane
D0005576cellular_componentextracellular region
D0005886cellular_componentplasma membrane
D0004872molecular_functionreceptor activity
D0006501biological_processC-terminal protein lipidation
D0007155biological_processcell adhesion
D0007342biological_processfusion of sperm to egg plasma membrane involved in single fertilization
D0007338biological_processsingle fertilization
D0035036biological_processsperm-egg recognition
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC13binding site for residue SO4 A 302
ChainResidue
ATHR194
AASP195
ALYS212

AC25binding site for residue CL B 302
ChainResidue
BTRP50
BSER100
BASN102
BASN217
BASN219

AC37binding site for residue SO4 D 302
ChainResidue
ACYS25
APRO27
AGLU80
ALEU83
ALYS154
DSER203
DARG205

AC45binding site for residue CL D 303
ChainResidue
DTRP50
DSER100
DASN102
DASN217
DASN219

AC52binding site for Mono-Saccharide NAG A 301 bound to ASN A 204
ChainResidue
ATRP202
AASN204

AC63binding site for Mono-Saccharide NAG B 301 bound to ASN B 73
ChainResidue
BLYS31
BPRO70
BASN73

AC72binding site for Mono-Saccharide NAG C 300 bound to ASN C 204
ChainResidue
CASN204
CTHR206

AC83binding site for Mono-Saccharide NAG D 301 bound to ASN D 73
ChainResidue
DLYS31
DPRO70
DASN73

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
NAG_5jke_A_3014N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
ATRP202-ASN204NAG: N-ACETYL-D-GLUCOSAMINE
ATHR206NAG: N-ACETYL-D-GLUCOSAMINE

NAG_5jke_B_3016N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
BLYS31-HIS32NAG: N-ACETYL-D-GLUCOSAMINE
BPRO70-LEU71NAG: N-ACETYL-D-GLUCOSAMINE
BASN73NAG: N-ACETYL-D-GLUCOSAMINE
BLYS163NAG: N-ACETYL-D-GLUCOSAMINE

NAG_5jke_C_3003N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
CTRP202NAG: N-ACETYL-D-GLUCOSAMINE
CASN204NAG: N-ACETYL-D-GLUCOSAMINE
CTHR206NAG: N-ACETYL-D-GLUCOSAMINE

NAG_5jke_D_3017N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
DLYS31-HIS32NAG: N-ACETYL-D-GLUCOSAMINE
DPRO70-ASN73NAG: N-ACETYL-D-GLUCOSAMINE
DLYS163NAG: N-ACETYL-D-GLUCOSAMINE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI121Helical. {ECO:0000255}.
ChainResidueDetails
ANA*

SWS_FT_FI221Helical. {ECO:0000255}.
ChainResidueDetails
CNA*

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb5jke.ent.gz (306.79 KB)
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all (no-compress)pdb5jke.ent (1.16 MB)
header onlypdb5jke.ent.gz (9.54 KB)
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PDBx/mmCIF5jke.cif.gz (359.64 KB)
PDBMLall5jke.xml.gz (493.56 KB)
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no-atom5jke-noatom.xml.gz (34.08 KB)
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ext-atom5jke-extatom.xml.gz (160.6 KB)
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PDBMLplusall5jke-plus.xml.gz (495.92 KB)
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no-atom5jke-plus-noatom.xml.gz (36.44 KB)
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add only5jke-add.xml.gz (2.37 KB)
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RDF5jke.rdf.gz (77.69 KB)
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Structure factorsr5jkesf.ent.gz (648.87 KB)
Biological unit (PDB format)5jke.pdb1.gz (151.55 KB) (A,B)
*author and software defined assembly, 2 molecule(s) (dimeric)
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5jke.pdb2.gz (151.85 KB) (C,D)
*author and software defined assembly, 2 molecule(s) (dimeric)
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Validation reportsPDF5jke​_validation.pdf.gz (481.8 KB)
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PDF-full5jke​_full​_validation.pdf.gz (491.63 KB)
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XML5jke​_validation.xml.gz (30.9 KB)
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PNG5jke​_multipercentile​_validation.png.gz (140.23 KB)
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SVG5jke​_multipercentile​_validation.svg.gz (950 B)
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Sequence (fasta)5jke​_seq.txt
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