1. The X-ray Crystal Structure of Full-Length Human Plasminogen
Ruby H.P. Law, Tom Caradoc-Davies, Nathan Cowieson, Anita J. Horvath, Adam J. Quek, Joanna Amarante Encarnacao, David Steer, Angus Cowan, Qingwei Zhang, Bernadine G.C. Lu, Robert N. Pike, A. Ian Smith, Paul B. Coughlin, James C. Whisstock 
Cell Reports 
Volume 1, Issue 3, Pages (March 2012)
DOI: /j.celrep
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2. Cell Reports 2012 1, 185-190DOI: (10.1016/j.celrep.2012.02.012)
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3. Figure 1
The Structure of Human Type II Plasminogen and the Interactions that Maintain the Closed Conformation
(A) The overall structure of plasminogen (molecule A). The domains are labeled and colored as follows: Pap, blue; KR1, pink; KR2, yellow; KR3, orange; KR4, green; KR5, purple; SP, cyan. Chloride ions Cl(1) and Cl(2) are at the KR4/PAp and KR2/SP interface, respectively, and are shown as spheres. Two other chloride ions, Cl(3) and Cl(4), bind to KR2 and SP domain, respectively. The position of the activation loop (R561) is marked with a red sphere. The LBS of KR1 is marked with an asterisk (∗).
(B) Key interactions made by the PAp domain with KR4 and KR5. K50 blocks the LBS of KR5 and primarily interacts with D518 of the DXD motif, forming an extremely short salt bridge (2.6Å). In contrast, D516 is ∼4 Å away. Arg70 coordinates both KR4 and KR5 through interactions with D413 and D534, respectively. Arg68 blocks the LBS of KR4, interacting with both D411 and D413 of the DXD motif. A chloride ion, Cl(1), forms hydrogen bonds with the backbone nitrogen (not shown) of R68 on the PAp domain, as well as the sidechains of R426 and K392. In the structure of KR4 bound to a C-terminal lysine analog (Wu et al., 1991), both R426 and K392 in KR4 function in binding the carboxylic acid group.
(C) Interface among KR4, the KR3/KR4 linker, the activation loop, and the SP domain. KR4 makes several interactions with the KR3/KR4 linker, mostly centered around residues 350–352. In contrast, only a single interaction between E554 of the activation loop and the backbone nitrogen of the KR3/KR4 linker residue V355 is apparent. Interestingly, T352 and P353 are mutated in plasminogen deficiency.
(D) The SP/KR2 interface – K708 from the SP domain is inserted into the LBS of KR2 and forms a salt bridge with both D219 and E221 of the DXE motif. A chloride ion, Cl(2), is coordinated by R234, W235 and the backbone nitrogen of K708. A salt bridge between R234 and E706 serves to tie the distal end of the LBS to the SP domain. D219 and R234 are both mutated in human disease (Schuster et al., 2007).
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4. Figure 2
The Influence of the N-Linked Glycosylation on Plasminogen Structure
(A) The KR3/SP interface. A hydrogen bond is formed between the δ-N of N289 on KR3 and the sidechain of E714 from the SP domain. Tyr713 from the SP domain is also at the interface.
(B) The low-resolution structure of type I plasminogen. KR3 is not visible in electron density; its position in type II plasminogen is indicated by an orange ellipse.
Cell Reports 2012 1, DOI: ( /j.celrep )
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5. Figure 3 The Activation Loop Is Shielded in the Closed State
(A) The activation loop (pink) and cleavage site (R561/V562—in stick) is protected by the position of the KR3/KR4 linker sequence. O-linked glycosylation on T346 in the KR3/KR4 linker further shields R561. The position of KR4, KR3, and the SP domain is shown.
(B) Superposition (made on the respective protease domains) of the structure of closed plasminogen with the previously reported structure of the miniplasmin/Streptokinase complex (PDB identifier 1BML) (Wang et al., 1998). Streptokinase (in red) binds in a fashion that avoids contact with the kringle array. The protease domain of the streptokinase complex structure is not shown.
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6. Figure 4 Kringle 5 Has Mobility with Respect to the PAp Domain
(A) Molecules A and B were superposed on PAp, KR1-4, and the SP domain. The figure illustrates the position of KR5 in molecule A (purple) with respect to molecule B (Red). The PAp domain of molecule B is also highlighted (blue). KR5 in molecule B has swung away from the PAp domain such that K50 (in stick, and labeled) is partially disordered but no longer docked in the KR5 LBS.
(B) Side-by-side comparison of the intact KR5 from molecule A and the partially disordered (start of such regions indicated by ∗) KR5 in molecule B. The two domains are similarly orientated. Disulphide bonds (yellow stick) are shown in each structure.
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7. Figure S1
The Plasminogen X-Ray Crystal Structure in the Context of a SAXS Envelope of Closed Plasminogen in Solution, Related to Figure 1
The de novo SAXS envelope model is the product of 10 DAMMIN runs that superimposed with an average NSD of and a maximum NSD of The averaged model was then run once more through DAMMIN giving a fit to the data of SQRT(chi) = The envelope SAXS model was superimposed onto the crystal structure using the program supcomb (Kozin and Svergun, 2000). Direct comparison of the crystal structure to the measured SAXS data using the program CRYSOL (Svergun et al., 1995) gives a fit of chi = 1.2.
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8. Figure S2
The Position of Human Mutations that Result in Severe Plasminogen Deficiency, Related to Figure 1
See Schuster et al., 2007.
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