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- PDB-7sa9: Human MUC16 SEA5 Domain -

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Basic information

Entry
Database: PDB / ID: 7sa9
TitleHuman MUC16 SEA5 Domain
ComponentsMucin-16
KeywordsUNKNOWN FUNCTION / Mucin / CA125 / ovarian cancer / pancreatic cancer
Function / homology
Function and homology information


Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / Dectin-2 family / Golgi lumen / vesicle / cell adhesion / external side of plasma membrane ...Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / Dectin-2 family / Golgi lumen / vesicle / cell adhesion / external side of plasma membrane / extracellular exosome / plasma membrane
Similarity search - Function
Mucin-16 / Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsBrooks, C.L. / White, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R15CA242349 United States
CitationJournal: Proteins / Year: 2022
Title: Crystal structure of a human MUC16 SEA domain reveals insight into the nature of the CA125 tumor marker.
Authors: White, B. / Patterson, M. / Karnwal, S. / Brooks, C.L.
History
DepositionSep 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mucin-16
B: Mucin-16


Theoretical massNumber of molelcules
Total (without water)41,4342
Polymers41,4342
Non-polymers00
Water3,675204
1
A: Mucin-16


Theoretical massNumber of molelcules
Total (without water)20,7171
Polymers20,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mucin-16


Theoretical massNumber of molelcules
Total (without water)20,7171
Polymers20,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.540, 90.145, 42.821
Angle α, β, γ (deg.)90.000, 102.877, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-286-

HOH

21A-292-

HOH

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Components

#1: Protein Mucin-16 / / MUC-16 / Ovarian cancer-related tumor marker CA125 / CA-125 / Ovarian carcinoma antigen CA125


Mass: 20717.180 Da / Num. of mol.: 2 / Fragment: SEA5 Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUC16, CA125 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8WXI7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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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: 1.78 Å3/Da / Density % sol: 31.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: ammonium acetate, PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.87 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.69→58.36 Å / Num. obs: 32113 / % possible obs: 98.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 24.06 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.05976 / Rpim(I) all: 0.03909 / Rrim(I) all: 0.07165 / Net I/σ(I): 9.74
Reflection shellResolution: 1.69→1.751 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.6197 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 10606 / CC1/2: 0.52 / CC star: 0.827 / Rrim(I) all: 0.3973 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MxDCdata collection
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IVZ

1ivz


Resolution: 1.69→58.36 Å / SU ML: 0.2485 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 25.7436
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.216 1603 5 %
Rwork0.2 30477 -
obs0.2009 32080 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.27 Å2
Refinement stepCycle: LAST / Resolution: 1.69→58.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 0 204 2108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411972
X-RAY DIFFRACTIONf_angle_d0.66982677
X-RAY DIFFRACTIONf_chiral_restr0.0412304
X-RAY DIFFRACTIONf_plane_restr0.0066346
X-RAY DIFFRACTIONf_dihedral_angle_d5.2984268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.69-1.740.35271560.34272742X-RAY DIFFRACTION97.15
1.74-1.810.33541320.31482724X-RAY DIFFRACTION97.51
1.81-1.880.35751470.31262734X-RAY DIFFRACTION97.89
1.88-1.970.27831570.26642722X-RAY DIFFRACTION98.13
1.97-2.070.25711460.21942791X-RAY DIFFRACTION98.69
2.07-2.20.20921380.19772752X-RAY DIFFRACTION98.7
2.2-2.370.21971410.19522797X-RAY DIFFRACTION98.72
2.37-2.610.19221140.18332786X-RAY DIFFRACTION99.08
2.61-2.980.18191560.18672791X-RAY DIFFRACTION99.46
2.98-3.760.19981540.17272798X-RAY DIFFRACTION99.53
3.76-58.360.19661620.18312840X-RAY DIFFRACTION99.63
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)
15.078881854256.410372622643.570882264158.96587053453.32258624613.92667123623-0.3556432553170.002353805826830.191726740391-0.3006305797370.152025801950.00714466194668-0.2951937894180.2603436358090.1697641633310.1860640090430.0174280033807-5.7112885836E-50.1638596653510.009513770071430.134780566671-1.35830803707-2.36251471418-6.11416485106
29.34073595338-3.170311117834.738034476687.09031564211-1.318066703884.510418820780.2081107868870.0476189819782-1.43351255276-0.01073261443460.08873285994690.01186112475420.832858629550.133798972006-0.2558252751530.4444893404840.01206822649180.08630585511070.2838197901290.01162072418550.468671867832-8.70451023583-21.5228373397-7.74008489468
33.80752240697-3.578225120951.600735064649.29531934697-3.384175088226.40801057004-0.009451348382980.0904984801686-0.250312795219-0.211308479751-0.005306642295830.09781326096820.5942586911980.02913086380330.03755062845480.197198252533-0.01515206316390.02545487238270.216403235167-0.03863049002580.116118294894-3.36224167294-10.3637753716-15.7307285474
49.16399700358-0.0145316680043-0.2154932822133.31684746432-0.3276401542454.40001002251-0.1467528531030.02980724969510.00328304314151-0.1223495227970.0673502386583-0.2806533896980.1867753745570.121952596930.0762736149820.15020526810.000162588763131-0.02020007233850.172765916631-0.01248856677680.0895560959540.2110859924180.32246963299-12.6242128047
55.696829699124.24442509624-1.582017723043.886891313-2.019700145533.94969225810.266281700481-0.342594195041-0.06436284453070.514269338596-0.2402229699930.6068182289620.37598284353-0.166312041355-0.04786843193870.2786210444710.02856687399690.07348419321610.209500268042-0.01500891011540.301856851567-8.57176537262-12.0305591484-4.74580859347
61.73968034933-3.50893981829-1.094226559287.241033776942.253075418050.7747291738410.410170061726-1.62543054061.05247278253-0.8404212219840.219590860116-1.14665530741-0.9698885678020.915958304761-0.5944818405710.434328536556-0.04981372620760.01563081338730.420083420565-0.1140464677950.6228674794473.232036386728.61013043636-7.74633118142
72.610325880140.245451991165-0.2962989044097.033930927722.527434101963.18172706451-0.1119594121570.08591906971650.0780568412874-0.0622658330537-0.06727662284110.451266926211-0.0882318039463-0.3652635719760.1736748951970.1368270782770.03846568782440.001467076191610.2369532402680.004336968006420.16442051474-14.9809190489-0.556844915683-8.5140117505
86.010647906931.170263612061.889096099384.1685833364-0.3857743412942.37125262957-0.007549901696640.86560422413-0.757374211856-0.141681822313-0.2893019566030.1780320835980.422942796403-0.03770979226040.2721382881670.32175773533-0.06137352059530.0440041406570.22221720483-0.031370887850.261388284166-12.2658786134-23.76604069086.23240562946
97.46034318887.22390371925-6.147206449857.19432000955-5.747449764985.659270492620.24861583591.093027375610.9577434026370.2435242894090.3011172482810.948330464995-0.388304001893-0.609126781194-0.4745761980620.245810570001-0.03769964775830.0257908001120.296583801885-0.03273091721420.335876423519-16.5322665345-6.4354209192710.7676484761
103.49095546112.36665485074-0.3347123954484.18861079162-3.481566649575.560635828080.237367038272-0.224914348921-0.232466313140.469853752617-0.0264108423723-0.1981256586780.269665763939-0.0293533379457-0.1863409318880.201214876546-0.0398072134792-0.0425381571650.230245841081-0.004358951544580.177053890778-10.5298675136-18.041366338616.2037595193
116.609576660763.07686216138-1.50467721214.33985921638-3.437875675322.92281674175-0.0480066446397-0.315668611928-0.7637050956310.314275369423-0.226034523333-1.388478009050.05924881543790.2105262571040.2497436996260.263422688099-0.0124043460098-0.03558860692440.29559466726-0.03454604408780.425796092665-7.09539163994-27.944535606611.5907308961
122.18435431130.553479876557-4.054755061726.393793112440.9284025144727.985344814190.1876197235481.35851097676-0.142088053205-0.600967469276-0.5116813381631.02820150318-0.0325066699394-1.036232268350.3049031390890.284486158283-0.0174109902679-0.07113623937460.335463006147-0.07003429628470.411472592833-21.2427971518-10.59295858336.40039665906
136.49536785034-6.88899249438-2.374999480067.850052073582.850792783324.12436722248-0.06099818868960.543729658669-0.4443070525020.746865309549-0.196221639032-0.3532058120230.5265042503570.1473333137460.2581635569480.30735003448-0.0915102874382-0.03254687749160.27861178438-0.03448842575040.426796817956-10.5932293291-21.92947211487.43711819538
144.041745944730.0553625403333-0.3191759345586.158695284590.5312031414153.95932881102-0.2831173692170.291844639496-0.606711657842-0.0195790000450.120534474199-0.1100036480230.39159567639-0.08147241813090.1691098188030.325395832629-0.1116525593680.04291500972290.232163652549-0.04930423716190.348019359938-16.0363946543-34.2100006377.78249500281
153.097119561291.4124537654-0.5559147545157.520316786623.30275219547.57686423337-0.01433378395150.06578888831860.0333780645934-0.163235272809-0.05899691588330.607233187056-0.0983371235282-0.2808553399740.04753386541350.188471367322-0.09178872510350.02740194469930.207863501099-0.02019128351380.253998173321-24.0747292777-24.40399742099.98619711845
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 35 through 47 )AA35 - 471 - 13
22chain 'A' and (resid 48 through 61 )AA48 - 6114 - 27
33chain 'A' and (resid 62 through 81 )AA62 - 8128 - 47
44chain 'A' and (resid 82 through 93 )AA82 - 9348 - 59
55chain 'A' and (resid 94 through 113 )AA94 - 11360 - 79
66chain 'A' and (resid 114 through 123 )AA114 - 12380 - 85
77chain 'A' and (resid 124 through 160 )AA124 - 16086 - 122
88chain 'B' and (resid 37 through 47 )BB37 - 471 - 11
99chain 'B' and (resid 48 through 61 )BB48 - 6112 - 25
1010chain 'B' and (resid 62 through 81 )BB62 - 8126 - 45
1111chain 'B' and (resid 82 through 93 )BB82 - 9346 - 57
1212chain 'B' and (resid 94 through 103 )BB94 - 10358 - 67
1313chain 'B' and (resid 104 through 114 )BB104 - 11468 - 78
1414chain 'B' and (resid 115 through 134 )BB115 - 13479 - 94
1515chain 'B' and (resid 135 through 160 )BB135 - 16095 - 120

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