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- EMDB-23057: rFVIIIFc-VWF-XTEN (BIVV001) -

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Basic information

Entry
Database: EMDB / ID: EMD-23057
TitlerFVIIIFc-VWF-XTEN (BIVV001)
Map dataFull map from 3D refinement
Sample
  • Complex: rFVIIIFc-VWF-XTEN (BIVV001)
    • Protein or peptide: Coagulation factor FVIII-Fc-XTEN
    • Protein or peptide: von Willebrand factor-XTEN-Fc
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
  • Ligand: COPPER (II) ION
Function / homology
Function and homology information


Defective F8 accelerates dissociation of the A2 domain / Defective F8 binding to the cell membrane / Defective F8 secretion / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Defective F8 sulfation at Y1699 / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective VWF binding to collagen type I / Weibel-Palade body / Defective F8 binding to von Willebrand factor ...Defective F8 accelerates dissociation of the A2 domain / Defective F8 binding to the cell membrane / Defective F8 secretion / Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation / Defective F8 sulfation at Y1699 / Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective VWF binding to collagen type I / Weibel-Palade body / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / hemostasis / blood coagulation, intrinsic pathway / platelet alpha granule / Platelet Adhesion to exposed collagen / Cargo concentration in the ER / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / COPII-mediated vesicle transport / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / COPII-coated ER to Golgi transport vesicle / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / immunoglobulin binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / Common Pathway of Fibrin Clot Formation / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / endoplasmic reticulum-Golgi intermediate compartment membrane / Integrin signaling / extracellular matrix / platelet alpha granule lumen / acute-phase response / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet activation / response to wounding / Golgi lumen / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / blood coagulation / integrin binding / Platelet degranulation / signaling receptor activity / protein-folding chaperone binding / collagen-containing extracellular matrix / protease binding / oxidoreductase activity / cell adhesion / copper ion binding / endoplasmic reticulum lumen / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Coagulation factor 5/8-like / von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. ...Coagulation factor 5/8-like / von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / C-terminal cystine knot signature. / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / Multicopper oxidase, C-terminal / Multicopper oxidase / von Willebrand factor type A domain / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Multicopper oxidase, N-terminal / Multicopper oxidase / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Cupredoxin / Galactose-binding-like domain superfamily
Similarity search - Domain/homology
Coagulation factor VIII / von Willebrand factor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsFuller JR / Batchelor JD
Citation
Journal: Elife / Year: 2016
Title: Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.
Authors: Ray Yu-Ruei Wang / Yifan Song / Benjamin A Barad / Yifan Cheng / James S Fraser / Frank DiMaio /
Abstract: Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5Å), providing biological phenomena with molecular descriptions. ...Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids - typical in a macromolecular assembly - is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.
#1: Journal: Comput. Cryst. Newsl. / Year: 2013
Title: New tool: phenix.real_space_refine
Authors: Afonine PV / Headd JJ / Terwilliger TC / Adams PD
History
DepositionDec 1, 2020-
Header (metadata) releaseMar 3, 2021-
Map releaseMar 3, 2021-
UpdateJun 9, 2021-
Current statusJun 9, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0145
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0145
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7kwo
  • Surface level: 0.0145
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23057.png

Downloads & links

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Map

FileDownload / File: emd_23057.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map from 3D refinement
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.0145 / Movie #1: 0.0145
Minimum - Maximum-0.03594801 - 0.08520259
Average (Standard dev.)-2.9564087e-06 (±0.001296866)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 407.03998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z407.040407.040407.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0360.085-0.000

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Supplemental data

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Mask #1

Fileemd_23057_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map sharpened by an automatically-fit B-factor (-69.3204) then...

Fileemd_23057_additional_1.map
AnnotationMap sharpened by an automatically-fit B-factor (-69.3204) then filtered to local resolution. Used for model building and refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map 2

Fileemd_23057_half_map_1.map
AnnotationUnfiltered half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map 1

Fileemd_23057_half_map_2.map
AnnotationUnfiltered half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : rFVIIIFc-VWF-XTEN (BIVV001)

EntireName: rFVIIIFc-VWF-XTEN (BIVV001)
Components
  • Complex: rFVIIIFc-VWF-XTEN (BIVV001)
    • Protein or peptide: Coagulation factor FVIII-Fc-XTEN
    • Protein or peptide: von Willebrand factor-XTEN-Fc
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
  • Ligand: COPPER (II) ION

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Supramolecule #1: rFVIIIFc-VWF-XTEN (BIVV001)

SupramoleculeName: rFVIIIFc-VWF-XTEN (BIVV001) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: An engineered therapeutic complex between coagulation factor VIII and von Willebrand factor D'D3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
Molecular weightTheoretical: 311.64974 KDa

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Macromolecule #1: Coagulation factor FVIII-Fc-XTEN

MacromoleculeName: Coagulation factor FVIII-Fc-XTEN / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 218.874969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQIELSTCFF LCLLRFCFSA TRRYYLGAVE LSWDYMQSDL GELPVDARFP PRVPKSFPFN TSVVYKKTLF VEFTDHLFNI AKPRPPWMG LLGPTIQAEV YDTVVITLKN MASHPVSLHA VGVSYWKASE GAEYDDQTSQ REKEDDKVFP GGSHTYVWQV L KENGPMAS ...String:
MQIELSTCFF LCLLRFCFSA TRRYYLGAVE LSWDYMQSDL GELPVDARFP PRVPKSFPFN TSVVYKKTLF VEFTDHLFNI AKPRPPWMG LLGPTIQAEV YDTVVITLKN MASHPVSLHA VGVSYWKASE GAEYDDQTSQ REKEDDKVFP GGSHTYVWQV L KENGPMAS DPLCLTYSYL SHVDLVKDLN SGLIGALLVC REGSLAKEKT QTLHKFILLF AVFDEGKSWH SETKNSLMQD RD AASARAW PKMHTVNGYV NRSLPGLIGC HRKSVYWHVI GMGTTPEVHS IFLEGHTFLV RNHRQASLEI SPITFLTAQT LLM DLGQFL LFCHISSHQH DGMEAYVKVD SCPEEPQLRM KNNEEAEDYD DDLTDSEMDV VRFDDDNSPS FIQIRSVAKK HPKT WVHYI AAEEEDWDYA PLVLAPDDRS YKSQYLNNGP QRIGRKYKKV RFMAYTDETF KTREAIQHES GILGPLLYGE VGDTL LIIF KNQASRPYNI YPHGITDVRP LYSRRLPKGV KHLKDFPILP GEIFKYKWTV TVEDGPTKSD PRCLTRYYSS FVNMER DLA SGLIGPLLIC YKESVDQRGN QIMSDKRNVI LFSVFDENRS WYLTENIQRF LPNPAGVQLE DPEFQASNIM HSINGYV FD SLQLSVCLHE VAYWYILSIG AQTDFLSVFF SGYTFKHKMV YEDTLTLFPF SGETVFMSME NPGLWILGCH NSDFRNRG M TALLKVSSCD KNTGDYYEDS YEDISAYLLS KNNAIEPRSF SQNGTSESAT PESGPGSEPA TSGSETPGTS ESATPESGP GSEPATSGSE TPGTSESATP ESGPGTSTEP SEGSAPGSPA GSPTSTEEGT SESATPESGP GSEPATSGSE TPGTSESATP ESGPGSPAG SPTSTEEGSP AGSPTSTEEG TSTEPSEGSA PGTSESATPE SGPGTSESAT PESGPGTSES ATPESGPGSE P ATSGSETP GSEPATSGSE TPGSPAGSPT STEEGTSTEP SEGSAPGTST EPSEGSAPGS EPATSGSETP GTSESATPES GP GTSTEPS EGSAPASSEI TRTTLQSDQE EIDYDDTISV EMKKEDFDI(TYS) DEDENQSPRS FQKKTRHYFI AAVERLWDY GMSSSPHVLR NRAQSGSVPQ FKKVVFQEFT DGSFTQPLYR GELNEHLGLL GPYIRAEVED NIMVTFRNQA SRPYSFYSSL ISYEEDQRQ GAEPRKNFVK PNETKTYFWK VQHHMAPTKD EFDCKAWAYF SDVDLEKDVH SGLIGPLLVC HTNTLNPAHG R QVTVQEFA LFFTIFDETK SWYFTENMER NCRAPCNIQM EDPTFKENYR FHAINGYIMD TLPGLVMAQD QRIRWYLLSM GS NENIHSI HFSGHVFTVR KKEEYKMALY NLYPGVFETV EMLPSKAGIW RVECLIGEHL HAGMSTLFLV YSNKCQTPLG MAS GHIRDF QITASGQYGQ WAPKLARLHY SGSINAWSTK EPFSWIKVDL LAPMIIHGIK TQGARQKFSS LYISQFIIMY SLDG KKWQT YRGNSTGTLM VFFGNVDSSG IKHNIFNPPI IARYIRLHPT HYSIRSTLRM ELMGCDLNSC SMPLGMESKA ISDAQ ITAS SYFTNMFATW SPSKARLHLQ GRSNAWRPQV NNPKEWLQVD FQKTMKVTGV TTQGVKSLLT SMYVKEFLIS SSQDGH QWT LFFQNGKVKV FQGNQDSFTP VVNSLDPPLL TRYLRIHPQS WVHQIALRME VLGCEAQDLY DKTHTCPPCP APELLGG PS VFLFPPKPKD TLMISRTPEV TCVVVDVSHE DPEVKFNWYV DGVEVHNAKT KPREEQYNST YRVVSVLTVL HQDWLNGK E YKCKVSNKAL PAPIEKTISK AKGQPREPQV YTLPPSRDEL TKNQVSLTCL VKGFYPSDIA VEWESNGQPE NNYKTTPPV LDSDGSFFLY SKLTVDKSRW QQGNVFSCSV MHEALHNHYT QKSLSLSPG

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Macromolecule #2: von Willebrand factor-XTEN-Fc

MacromoleculeName: von Willebrand factor-XTEN-Fc / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 179.048953 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MIPARFAGVL LALALILPGT LCAEGTRGRS STARCSLFGS DFVNTFDGSM YSFAGYCSYL LAGGCQKRSF SIIGDFQNGK RVSLSVYLG EFFDIHLFVN GTVTQGDQRV SMPYASKGLY LETEAGYYKL SGEAYGFVAR IDGSGNFQVL LSDRYFNKTC G LCGNFNIF ...String:
MIPARFAGVL LALALILPGT LCAEGTRGRS STARCSLFGS DFVNTFDGSM YSFAGYCSYL LAGGCQKRSF SIIGDFQNGK RVSLSVYLG EFFDIHLFVN GTVTQGDQRV SMPYASKGLY LETEAGYYKL SGEAYGFVAR IDGSGNFQVL LSDRYFNKTC G LCGNFNIF AEDDFMTQEG TLTSDPYDFA NSWALSSGEQ WCERASPPSS SCNISSGEMQ KGLWEQCQLL KSTSVFARCH PL VDPEPFV ALCEKTLCEC AGGLECACPA LLEYARTCAQ EGMVLYGWTD HSACSPVCPA GMEYRQCVSP CARTCQSLHI NEM CQERCV DGCSCPEGQL LDEGLCVEST ECPCVHSGKR YPPGTSLSRD CNTCICRNSQ WICSNEECPG ECLVTGQSHF KSFD NRYFT FSGICQYLLA RDCQDHSFSI VIETVQCADD RDAVCTRSVT VRLPGLHNSL VKLKHGAGVA MDGQDIQLPL LKGDL RIQH TVTASVRLSY GEDLQMDWDG RGRLLVKLSP VYAGKTCGLC GNYNGNQGDD FLTPSGLAEP RVEDFGNAWK LHGDCQ DLQ KQHSDPCALN PRMTRFSEEA CAVLTSPTFE ACHRAVSPLP YLRNCRYDVC SCSDGRECLC GALASYAAAC AGRGVRV AW REPGRCELNC PKGQVYLQCG TPCNLTCRSL SYPDEECNEA CLEGCFCPPG LYMDERGDCV PKAQCPCYYD GEIFQPED I FSDHHTMCYC EDGFMHCTMS GVPGSLLPDA VLSSPLSHRS KRSLSCRPPM VKLVCPADNL RAEGLECTKT CQNYDLECM SMGCVSGCLC PPGMVRHENR CVALERCPCF HQGKEYAPGE TVKIGCNTCV CRDRKWNCTD HVCDATCSTI GMAHYLTFDG LKYLFPGEC QYVLVQDYCG SNPGTFRILV GNKGCSHPSV KCKKRVTILV EGGEIELFDG EVNVKRPMKD ETHFEVVESG R YIILLLGK ALSVVWDRHL SISVVLKQTY QEKVCGLCGN FDGIQNNDLT SSNLQVEEDP VDFGNSWKVS SQCADTRKVP LD SSPATCH NNIMKQTMVD SSCRILTSDV FQDCNKLVDP EPYLDVCIYD TCSCESIGDC AAFCDTIAAY AHVCAQHGKV VTW RTATLC PQSCEERNLR ENGYEAEWRY NSCAPACQVT CQHPEPLACP VQCVEGCHAH CPPGKILDEL LQTCVDPEDC PVCE VAGRR FASGKKVTLN PSDPEHCQIC HCDVVNLTCE ACQEPGTSES ATPESGPGSE PATSGSETPG TSESATPESG PGSEP ATSG SETPGTSESA TPESGPGTST EPSEGSAPGS PAGSPTSTEE GTSESATPES GPGSEPATSG SETPGTSESA TPESGP GSP AGSPTSTEEG SPAGSPTSTE EGASSDKNTG DYYEDSYEDI SAYLLSKNNA IEPRSFSDKT HTCPPCPAPE LLGGPSV FL FPPKPKDTLM ISRTPEVTCV VVDVSHEDPE VKFNWYVDGV EVHNAKTKPR EEQYNSTYRV VSVLTVLHQD WLNGKEYK C KVSNKALPAP IEKTISKAKG QPREPQVYTL PPSRDELTKN QVSLTCLVKG FYPSDIAVEW ESNGQPENNY KTTPPVLDS DGSFFLYSKL TVDKSRWQQG NVFSCSVMHE ALHNHYTQKS LSLSPG

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation #1

Preparation ID1
Concentration0.75 mg/mL
BufferpH: 7.3
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
2.5 mMCaCl2calcium chloride
25.0 mMC8H18N2O4SHEPES
0.0038 %C15H24O(C2H4O)nNP-40 Alternative (CAS 9016-45-9)

Details: NP-40s detergent was added to samples immediately prior to vitrification, to a final concentration of 0.0038 % (weight/volume).
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Film type ID: 1 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV
DetailsPrepared by gel filtration chromatography immediately prior to vitrification.

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Sample preparation #2

Preparation ID2
Concentration0.75 mg/mL
BufferpH: 7.3
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
2.5 mMCaCl2calcium chloride
25.0 mMC8H18N2O4SHEPES
0.0038 %C15H24O(C2H4O)nNP-40 Alternative (CAS 9016-45-9)

Details: NP-40s detergent was added to samples immediately prior to vitrification, to a final concentration of 0.0038 % (weight/volume).
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Film type ID: 1 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV
DetailsPrepared by gel filtration chromatography immediately prior to vitrification.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsMicrograph movies were motion-corrected and dose-weighted using Relion 3.0
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.13)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 116200
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM (ver. 1.0.0beta)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6mf2

chain_id: A

6n29

chain_id: V
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7kwo:
rFVIIIFc-VWF-XTEN (BIVV001)

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