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- PDB-6ndh: RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN AND ZINC -

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Basic information

Entry
Database: PDB / ID: 6ndh
TitleRHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN AND ZINC
Components
  • (Snaclec rhodocetin subunit ...) x 2
  • Integrin alpha-2
KeywordsCELL ADHESION/TOXIN / C-TYPE LECTIN / INTEGRIN / VENOM / COAGULATION / CELL ADHESION / CELL ADHESION-TOXIN complex
Function / homology
Function and homology information


collagen receptor activity / substrate-dependent cell migration / positive regulation of cell projection organization / positive regulation of transmission of nerve impulse / response to parathyroid hormone / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / hypotonic response / response to L-ascorbic acid / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition ...collagen receptor activity / substrate-dependent cell migration / positive regulation of cell projection organization / positive regulation of transmission of nerve impulse / response to parathyroid hormone / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / hypotonic response / response to L-ascorbic acid / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / CHL1 interactions / skin morphogenesis / Laminin interactions / positive regulation of smooth muscle contraction / collagen-activated signaling pathway / basal part of cell / positive regulation of phagocytosis, engulfment / Platelet Adhesion to exposed collagen / hepatocyte differentiation / mammary gland development / focal adhesion assembly / mesodermal cell differentiation / heparan sulfate proteoglycan binding / positive regulation of leukocyte migration / positive regulation of positive chemotaxis / integrin complex / MET activates PTK2 signaling / cell adhesion mediated by integrin / Syndecan interactions / response to muscle activity / positive regulation of smooth muscle cell migration / cell-substrate adhesion / response to amine / positive regulation of collagen biosynthetic process / positive regulation of epithelial cell migration / ECM proteoglycans / Integrin cell surface interactions / detection of mechanical stimulus involved in sensory perception of pain / laminin binding / collagen binding / axon terminus / extracellular matrix organization / positive regulation of cell adhesion / cell-matrix adhesion / positive regulation of translation / animal organ morphogenesis / integrin-mediated signaling pathway / female pregnancy / positive regulation of smooth muscle cell proliferation / cellular response to estradiol stimulus / cell-cell adhesion / cellular response to mechanical stimulus / blood coagulation / integrin binding / amyloid-beta binding / virus receptor activity / toxin activity / response to hypoxia / cell adhesion / response to xenobiotic stimulus / external side of plasma membrane / focal adhesion / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
: / Integrin alpha Ig-like domain 3 / : / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. ...: / Integrin alpha Ig-like domain 3 / : / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / C-type lectin, conserved site / C-type lectin domain signature. / FG-GAP repeat / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AMMONIUM ION / Snaclec rhodocetin subunit gamma / Snaclec rhodocetin subunit delta / Integrin alpha-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Calloselasma rhodostoma (Malayan pit viper)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsStetefeld, J. / McDougall, M.D. / Loewen, P.C.
CitationJournal: To be published
Title: RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN WITH ZINC BOUND
Authors: Stetefeld, J. / McDougall, M.D. / Loewen, P.C.
History
DepositionDec 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Snaclec rhodocetin subunit gamma
B: Snaclec rhodocetin subunit delta
C: Integrin alpha-2
D: Snaclec rhodocetin subunit gamma
E: Snaclec rhodocetin subunit delta
F: Integrin alpha-2
G: Snaclec rhodocetin subunit gamma
H: Snaclec rhodocetin subunit delta
I: Integrin alpha-2
J: Snaclec rhodocetin subunit gamma
K: Snaclec rhodocetin subunit delta
L: Integrin alpha-2
M: Snaclec rhodocetin subunit gamma
N: Snaclec rhodocetin subunit delta
O: Integrin alpha-2
P: Snaclec rhodocetin subunit gamma
Q: Snaclec rhodocetin subunit delta
R: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)328,44055
Polymers326,13118
Non-polymers2,30837
Water1267
1
A: Snaclec rhodocetin subunit gamma
B: Snaclec rhodocetin subunit delta
C: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,80310
Polymers54,3553
Non-polymers4477
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-123 kcal/mol
Surface area20270 Å2
MethodPISA
2
D: Snaclec rhodocetin subunit gamma
E: Snaclec rhodocetin subunit delta
F: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,78510
Polymers54,3553
Non-polymers4307
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-133 kcal/mol
Surface area20320 Å2
MethodPISA
3
G: Snaclec rhodocetin subunit gamma
H: Snaclec rhodocetin subunit delta
I: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6718
Polymers54,3553
Non-polymers3165
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-122 kcal/mol
Surface area20250 Å2
MethodPISA
4
J: Snaclec rhodocetin subunit gamma
K: Snaclec rhodocetin subunit delta
L: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,74210
Polymers54,3553
Non-polymers3877
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-123 kcal/mol
Surface area20270 Å2
MethodPISA
5
M: Snaclec rhodocetin subunit gamma
N: Snaclec rhodocetin subunit delta
O: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6718
Polymers54,3553
Non-polymers3165
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-119 kcal/mol
Surface area20230 Å2
MethodPISA
6
P: Snaclec rhodocetin subunit gamma
Q: Snaclec rhodocetin subunit delta
R: Integrin alpha-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7679
Polymers54,3553
Non-polymers4126
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-115 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.399, 131.399, 251.358
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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Snaclec rhodocetin subunit ... , 2 types, 12 molecules ADGJMPBEHKNQ

#1: Protein
Snaclec rhodocetin subunit gamma


Mass: 15741.510 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Calloselasma rhodostoma (Malayan pit viper)
References: UniProt: D2YW39
#2: Protein
Snaclec rhodocetin subunit delta


Mass: 14875.982 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Calloselasma rhodostoma (Malayan pit viper)
References: UniProt: D2YW40

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Protein , 1 types, 6 molecules CFILOR

#3: Protein
Integrin alpha-2 / CD49 antigen-like family member B / Collagen receptor / Platelet membrane glycoprotein Ia / GPIa / ...CD49 antigen-like family member B / Collagen receptor / Platelet membrane glycoprotein Ia / GPIa / VLA-2 subunit alpha


Mass: 23737.738 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGA2, CD49B / Production host: Escherichia coli (E. coli) / References: UniProt: P17301

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Non-polymers , 6 types, 44 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.52 Å3/Da / Density % sol: 65.04 % / Mosaicity: 0.21 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M TRIS, 2.65 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 27, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.9→131.399 Å / Num. obs: 92641 / % possible obs: 98.6 % / Redundancy: 7.8 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.095 / Rsym value: 0.089 / Net I/av σ(I): 8.2 / Net I/σ(I): 18.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.9-3.067.80.5521.4134150.210.590.55297.6
3.06-3.247.80.3252.4126270.1240.3480.32597.9
3.24-3.477.80.2043.8119950.0780.2180.20498.2
3.47-3.747.80.1216.4111740.0460.130.12198.5
3.74-4.17.80.0858.9103160.0330.0910.08598.8
4.1-4.597.70.0612.293500.0230.0640.0699
4.59-5.297.70.05313.682850.0210.0570.05399.3
5.29-6.487.70.05612.870160.0220.060.05699.5
6.48-9.177.60.0381754700.0150.040.03899.8
9.17-46.9537.20.02822.629930.0110.0310.02899.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5THP

5thp


Resolution: 2.9→47 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.869 / SU B: 18.846 / SU ML: 0.352 / SU R Cruickshank DPI: 2.4092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.409 / ESU R Free: 0.418 / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2849 4534 4.9 %RANDOM
Rwork0.2282 ---
obs0.2311 88062 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 181.99 Å2 / Biso mean: 55.617 Å2 / Biso min: 20.18 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2--1.09 Å20 Å2
3----2.18 Å2
Refinement stepCycle: final / Resolution: 2.9→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21486 0 97 7 21590
Biso mean--80.26 30.28 -
Num. residues----2664
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01322128
X-RAY DIFFRACTIONr_bond_other_d0.0010.01819668
X-RAY DIFFRACTIONr_angle_refined_deg1.371.63729994
X-RAY DIFFRACTIONr_angle_other_deg1.1661.57945618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.27152646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66522.4631218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.46153708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.28215132
X-RAY DIFFRACTIONr_chiral_restr0.0470.22766
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0224744
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025028
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 318 -
Rwork0.328 6469 -
all-6787 -
obs--97.58 %

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